id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19314 ChimeraX bug report submission banco.miket@… "{{{ The following bug report has been submitted: Platform: macOS-26.0.1-arm64-arm-64bit ChimeraX Version: 1.10rc202505150242 (2025-05-15 02:42:12 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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All rights reserved. How to cite UCSF ChimeraX > open /Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Refine_52/ADPR-TK2284-NEB7-5_refine_052.pdb Chain information for ADPR-TK2284-NEB7-5_refine_052.pdb #1 --- Chain | Description D | No description available E | No description available L | No description available M | No description available N | No description available O | No description available 8 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > set bgColor white > lighting soft > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Refine_52/ADPR-TK2284-NEB7-5_refine_052 copy.pdb"" Chain information for ADPR-TK2284-NEB7-5_refine_052 copy.pdb #2 --- Chain | Description D | No description available E | No description available L | No description available M | No description available N | No description available O | No description available 8 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #2 models > show #2 models > hide atoms > show cartoons Computing secondary structure > dssp > set bgColor white > lighting soft > graphics silhouettes true > select #1/M:157 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 63 atoms, 63 bonds, 8 residues, 1 model selected > select up 994 atoms, 1013 bonds, 130 residues, 1 model selected > delete atoms sel > delete bonds sel > hide #2 models > select #1/L:83 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 107 atoms, 106 bonds, 13 residues, 1 model selected > select up 990 atoms, 1009 bonds, 128 residues, 1 model selected > delete sel Drag select of 74 residues > delete sel > select clear > show #2 models > hide #1 models > hide #2 models > show #2 models > hide #2 models > show #1 models > show #2 models > hide #2 models > show #2 models > hide #1 models > select #2/O:47 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 61 atoms, 60 bonds, 9 residues, 1 model selected > select up 1276 atoms, 1301 bonds, 166 residues, 1 model selected > delete sel > select #2/N:86 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 103 atoms, 102 bonds, 13 residues, 1 model selected > select up 1266 atoms, 1291 bonds, 166 residues, 1 model selected > delete sel > show #1 models > select #1/N 1266 atoms, 1291 bonds, 166 residues, 1 model selected > select ~sel & ##selected 1738 atoms, 1393 bonds, 540 residues, 1 model selected > select ~sel & ##selected 1266 atoms, 1291 bonds, 166 residues, 1 model selected > select #1/N:39-400 #2/L:39-300 1969 atoms, 2007 bonds, 256 residues, 2 models selected > ui tool show Matchmaker > matchmaker #2 & sel to #1 & sel Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ADPR-TK2284-NEB7-5_refine_052.pdb, chain N (#1) with ADPR- TK2284-NEB7-5_refine_052 copy.pdb, chain L (#2), sequence alignment score = 646.4 RMSD between 128 pruned atom pairs is 0.177 angstroms; (across all 128 pairs: 0.177) > matchmaker #2 & sel to #1 & sel Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ADPR-TK2284-NEB7-5_refine_052.pdb, chain N (#1) with ADPR- TK2284-NEB7-5_refine_052 copy.pdb, chain L (#2), sequence alignment score = 646.4 RMSD between 128 pruned atom pairs is 0.177 angstroms; (across all 128 pairs: 0.177) > color #1 #ff9300ff > color #2 #008f00ff > ui mousemode right zoom > select clear > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/8oxoATP + Ca/DONT USE > MY MODEL/Ca_8oxoATP_refine_033-FINAL.pdb"" Chain information for Ca_8oxoATP_refine_033-FINAL.pdb #3 --- Chain | Description A | No description available B | No description available > mmaker #1 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Ca_8oxoATP_refine_033-FINAL.pdb, chain A (#3) with ADPR- TK2284-NEB7-5_refine_052.pdb, chain O (#1), sequence alignment score = 844.4 RMSD between 156 pruned atom pairs is 0.545 angstroms; (across all 166 pairs: 1.002) > hide #2 models Drag select of 14 residues > select clear > dssp > color #3 #0433ffff > color #3 #0096ffff > select clear Drag select of 6 residues > select rib Expected an objects specifier or a keyword > select ::name=""RIB"" 184 atoms, 184 bonds, 8 residues, 2 models selected > show sel & #1 atoms > select clear > ui tool show ""Side View"" > show #2 models > hide #2 models > select :60 49 atoms, 40 bonds, 9 residues, 3 models selected > show sel & #1,3 atoms > style sel & #1,3 stick Changed 34 atom styles > select :134 48 atoms, 39 bonds, 9 residues, 3 models selected > show sel & #1,3 atoms > select ~sel & ##selected 8666 atoms, 7979 bonds, 1844 residues, 3 models selected > select ~sel & ##selected 48 atoms, 39 bonds, 9 residues, 3 models selected > select up 347 atoms, 338 bonds, 55 residues, 3 models selected > select :135 47 atoms, 39 bonds, 8 residues, 3 models selected > show sel & #1,3 atoms > style sel & #1,3 stick Changed 30 atom styles > select #1/N:134@CB 1 atom, 1 residue, 1 model selected > select #1/N:134@CA 1 atom, 1 residue, 1 model selected > style sel stick Changed 1 atom style > select clear > select :134 48 atoms, 39 bonds, 9 residues, 3 models selected > hide sel & #1,3 atoms Drag select of 2 residues, 1 atoms > select up 95 atoms, 96 bonds, 13 residues, 2 models selected > select up 2546 atoms, 2595 bonds, 334 residues, 2 models selected > select up 2582 atoms, 2629 bonds, 339 residues, 2 models selected > select clear > show #1,3 atoms > style #1,3 stick Changed 5711 atom styles > select :138 52 atoms, 44 bonds, 8 residues, 3 models selected > show target m > hide #2 models > select clear > hide #1,3 atoms > select :138 52 atoms, 44 bonds, 8 residues, 3 models selected > show sel & #1,3 atoms Drag select of 75 residues > select :138 52 atoms, 44 bonds, 8 residues, 3 models selected > show sel & #1,3 atoms > select up 368 atoms, 372 bonds, 49 residues, 3 models selected > select down 52 atoms, 44 bonds, 8 residues, 3 models selected > select clear > select :135-140 286 atoms, 275 bonds, 47 residues, 3 models selected > show sel & #1,3 atoms > close > close # Expected a models specifier or a keyword > open /Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/ADPR-TK2284-NEB7-5_refine_052-coot-0.pdb Chain information for ADPR-TK2284-NEB7-5_refine_052-coot-0.pdb #1 --- Chain | Description D | No description available E | No description available L | No description available M | No description available N | No description available O | No description available 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Drag select of 158 atoms, 17 bonds > select clear > hide cartoons > hide surfaces > show cartoons Computing secondary structure > hide surfaces > hide atoms > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/8oxoATP + > Ca/MyModel/Ca_8oxoATP_refine_033-FINAL.pdb"" Chain information for Ca_8oxoATP_refine_033-FINAL.pdb #2 --- Chain | Description A | No description available B | No description available > hide #1 models > select :137 43 atoms, 36 bonds, 7 residues, 2 models selected > select :91 56 atoms, 48 bonds, 8 residues, 2 models selected > show sel & #2 atoms > open /Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Model-Removed-H.pdb Chain information for Model-Removed-H.pdb #3 --- Chain | Description L | No description available M | No description available N | No description available O | No description available 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > close > open /Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Refine_61/ADPR-TK2284-NEB7-5_refine_061.pdb Chain information for ADPR-TK2284-NEB7-5_refine_061.pdb #1 --- Chain | Description L | No description available M | No description available N | No description available O | No description available 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > dssp > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/Comparison > of Substrate Binding.cxs"" > view name session-start opened ChimeraX session > show #!2 models > hide #1 models > open /Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Refine_61/ADPR-TK2284-NEB7-5_refine_061.pdb Chain information for ADPR-TK2284-NEB7-5_refine_061.pdb #5 --- Chain | Description L | No description available M | No description available N | No description available O | No description available 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > select add #2 2938 atoms, 2874 bonds, 482 residues, 1 model selected > show sel cartoons > select #5/N 1273 atoms, 1298 bonds, 166 residues, 1 model selected > select #5/N #2 4211 atoms, 4172 bonds, 648 residues, 2 models selected > mmaker sele > matchmaker sele Missing or invalid ""matchAtoms"" argument: invalid atoms specifier > mmaker select > matchmaker select Missing or invalid ""matchAtoms"" argument: invalid atoms specifier > ui tool show Matchmaker > matchmaker #5 & sel to #2 & sel ssFraction 0.7122 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.7122 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2qjo(NadM).pdb, chain B (#2) with ADPR- TK2284-NEB7-5_refine_061.pdb, chain N (#5), sequence alignment score = 380.183 RMSD between 56 pruned atom pairs is 0.836 angstroms; (across all 146 pairs: 13.312) > select #2/B:219 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > close #1,5#2-4 > open /Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Refine_61/ADPR-TK2284-NEB7-5_refine_061.pdb Chain information for ADPR-TK2284-NEB7-5_refine_061.pdb #1 --- Chain | Description L | No description available M | No description available N | No description available O | No description available 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB > Files/2qjo(NadM).pdb"" 2qjo(NadM).pdb title: Crystal structure of A bifunctional NMN adenylyltransferase/adp ribose pyrophosphatase (nadm) complexed with adprp and nad from synechocystis SP. [more info...] Chain information for 2qjo(NadM).pdb #2 --- Chain | Description | UniProt A B C | bifunctional NMN adenylyltransferase/nudix hydrolase | NADM_SYNY3 1-339 Non-standard residues in 2qjo(NadM).pdb #2 --- APR — adenosine-5-diphosphoribose NAD — nicotinamide-adenine-dinucleotide POP — pyrophosphate 2- SO4 — sulfate ion 26 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select #2/C:315 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 55 atoms, 55 bonds, 7 residues, 1 model selected > select up 264 atoms, 273 bonds, 30 residues, 1 model selected > select up 323 atoms, 333 bonds, 39 residues, 1 model selected > select up 2639 atoms, 2711 bonds, 327 residues, 1 model selected > delete select Missing or invalid ""atoms"" argument: invalid atoms specifier > delete sel > select #2/A:243 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 124 atoms, 123 bonds, 15 residues, 1 model selected > select up 2423 atoms, 2487 bonds, 303 residues, 1 model selected > delete sel > select clear > select #2/B:98 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 139 atoms, 140 bonds, 18 residues, 1 model selected > select up 2702 atoms, 2775 bonds, 336 residues, 1 model selected > select clear Drag select of 125 atoms, 125 bonds > select clear Drag select of 93 atoms, 95 bonds > delete sel Drag select of 41 atoms, 39 bonds > delete sel Drag select of 58 atoms, 56 bonds > delete sel Drag select of 6 atoms, 4 bonds > delete sel > select #1/N #2 4635 atoms, 4447 bonds, 835 residues, 2 models selected > ui tool show Matchmaker > matchmaker #!2 & sel to #1 & sel ssFraction 0.7122 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.7122 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain N (#1) with 2qjo(NadM).pdb, chain B (#2), sequence alignment score = 380.183 RMSD between 56 pruned atom pairs is 0.836 angstroms; (across all 146 pairs: 13.312) > select clear > select #2/B:96 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 139 atoms, 140 bonds, 18 residues, 1 model selected > select up 2702 atoms, 2775 bonds, 336 residues, 1 model selected > select #1/N #2 4635 atoms, 4447 bonds, 835 residues, 2 models selected > select clear > select #2/B:128 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 37 atoms, 37 bonds, 4 residues, 1 model selected > select up 2702 atoms, 2775 bonds, 336 residues, 1 model selected > delete sel > select clear > select #2/A:329 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 91 atoms, 94 bonds, 10 residues, 1 model selected > select up 258 atoms, 267 bonds, 29 residues, 1 model selected > delete sel Drag select of 61 atoms, 60 bonds > delete sel Drag select of 14 atoms, 8 bonds > delete sel > select #1/A:4@C04 1 atom, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > delete sel > save /Users/mbanco/Documents/Science/TK2284/Structures/Combined- > TK2284-NadM.pdb > save /Users/mbanco/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Combined-TK2284-NadM.pdb displayedOnly true > open /Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Combined-TK2284-NadM.pdb Summary of feedback from opening /Users/mbanco/Library/CloudStorage/OneDrive- NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- NEB7-5/Combined-TK2284-NadM.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 SER L 17 LYS L 29 1 13 Start residue of secondary structure not found: HELIX 2 2 VAL L 81 THR L 93 1 13 Start residue of secondary structure not found: HELIX 3 3 ILE L 144 GLU L 146 1 3 Start residue of secondary structure not found: HELIX 4 4 ALA L 147 ASN L 149 1 3 End residue of secondary structure not found: HELIX 5 5 HIS L 156 ALA L 163 1 8 Start residue of secondary structure not found: HELIX 6 6 ALA M 17 LYS M 29 1 13 Start residue of secondary structure not found: HELIX 7 7 VAL M 81 THR M 93 1 13 Start residue of secondary structure not found: HELIX 8 8 ILE M 144 GLU M 146 1 3 Start residue of secondary structure not found: HELIX 9 9 ALA M 147 ASN M 149 1 3 End residue of secondary structure not found: HELIX 10 10 HIS M 156 ALA M 163 1 8 Start residue of secondary structure not found: HELIX 11 11 SER N 17 LYS N 29 1 13 Start residue of secondary structure not found: HELIX 12 12 VAL N 81 THR N 93 1 13 Start residue of secondary structure not found: HELIX 13 13 ILE N 144 GLU N 146 1 3 Start residue of secondary structure not found: HELIX 14 14 ALA N 147 ASN N 149 1 3 End residue of secondary structure not found: HELIX 15 15 HIS N 156 ALA N 163 1 8 Start residue of secondary structure not found: HELIX 16 16 ALA O 17 ALA O 27 1 11 Start residue of secondary structure not found: HELIX 17 17 GLU O 28 TYR O 30 1 3 Start residue of secondary structure not found: HELIX 18 18 VAL O 81 THR O 93 1 13 Start residue of secondary structure not found: HELIX 19 19 ILE O 144 GLU O 146 1 3 Start residue of secondary structure not found: HELIX 20 20 ALA O 147 ASN O 149 1 3 End residue of secondary structure not found: HELIX 21 21 HIS O 156 ALA O 163 1 8 Start residue of secondary structure not found: SHEET 1 1 1 ASP L 2 LYS L 9 0 Start residue of secondary structure not found: SHEET 2 2 1 GLY L 41 VAL L 49 0 Start residue of secondary structure not found: SHEET 3 3 1 GLY L 53 ARG L 59 0 End residue of secondary structure not found: SHEET 4 4 1 GLY L 72 PHE L 74 0 Start residue of secondary structure not found: SHEET 5 5 1 ASP L 96 LEU L 102 0 Start residue of secondary structure not found: SHEET 6 6 1 GLY L 104 TYR L 106 0 Start residue of secondary structure not found: SHEET 7 7 1 THR L 117 ALA L 121 0 Start residue of secondary structure not found: SHEET 8 8 1 PHE L 122 GLU L 127 0 Start residue of secondary structure not found: SHEET 9 9 1 ALA L 136 PRO L 143 0 4 messages similar to the above omitted End residue of secondary structure not found: SHEET 14 14 1 GLY M 72 PHE M 74 0 Start residue of secondary structure not found: SHEET 15 15 1 LEU M 95 LEU M 102 0 Start residue of secondary structure not found: SHEET 16 16 1 GLY M 104 TYR M 106 0 Start residue of secondary structure not found: SHEET 17 17 1 THR M 117 ALA M 121 0 Start residue of secondary structure not found: SHEET 18 18 1 PHE M 122 GLY M 128 0 Start residue of secondary structure not found: SHEET 19 19 1 ALA M 136 PHE M 142 0 4 messages similar to the above omitted End residue of secondary structure not found: SHEET 24 24 1 GLY N 72 PHE N 74 0 Start residue of secondary structure not found: SHEET 25 25 1 LEU N 95 LEU N 102 0 Start residue of secondary structure not found: SHEET 26 26 1 GLY N 104 TYR N 106 0 Start residue of secondary structure not found: SHEET 27 27 1 THR N 117 ALA N 121 0 Start residue of secondary structure not found: SHEET 28 28 1 PHE N 122 GLY N 128 0 Start residue of secondary structure not found: SHEET 29 29 1 ALA N 136 PHE N 142 0 4 messages similar to the above omitted End residue of secondary structure not found: SHEET 34 34 1 GLY O 72 PHE O 74 0 Start residue of secondary structure not found: SHEET 35 35 1 LEU O 95 LEU O 102 0 Start residue of secondary structure not found: SHEET 36 36 1 GLY O 104 TYR O 106 0 Start residue of secondary structure not found: SHEET 37 37 1 THR O 117 ALA O 121 0 Start residue of secondary structure not found: SHEET 38 38 1 PHE O 122 GLY O 128 0 Start residue of secondary structure not found: SHEET 39 39 1 ALA O 136 PHE O 142 0 Cannot find LINK/SSBOND residue CYS (39 ) Cannot find LINK/SSBOND residue CYS (39 ) Start residue of secondary structure not found: HELIX 1 1 SER L 17 LYS L 29 1 13 Start residue of secondary structure not found: HELIX 2 2 VAL L 81 THR L 93 1 13 Start residue of secondary structure not found: HELIX 3 3 ILE L 144 GLU L 146 1 3 Start residue of secondary structure not found: HELIX 4 4 ALA L 147 ASN L 149 1 3 Start residue of secondary structure not found: HELIX 5 5 HIS L 156 ALA L 163 1 8 55 messages similar to the above omitted Chain information for Combined-TK2284-NadM.pdb --- Chain | Description 3.1/L | No description available 3.1/M | No description available 3.1/N | No description available 3.1/O | No description available Computing secondary structure > hide #!3.1 models > hide #1 models > hide #!2 models > hide #!3 models > show #!3.1 models > hide #!3 models > show #!3 models > close #3 > show #1 models > show #!2 models > select clear > save /Users/mbanco/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Combined-TK2284-NadM.pdb > open /Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Combined-TK2284-NadM.pdb Summary of feedback from opening /Users/mbanco/Library/CloudStorage/OneDrive- NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- NEB7-5/Combined-TK2284-NadM.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 SER L 17 LYS L 29 1 13 Start residue of secondary structure not found: HELIX 2 2 VAL L 81 THR L 93 1 13 Start residue of secondary structure not found: HELIX 3 3 ILE L 144 GLU L 146 1 3 Start residue of secondary structure not found: HELIX 4 4 ALA L 147 ASN L 149 1 3 Start residue of secondary structure not found: HELIX 5 5 HIS L 156 ALA L 163 1 8 55 messages similar to the above omitted 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for Combined-TK2284-NadM.pdb --- Chain | Description 3.1/L | No description available 3.1/M | No description available 3.1/N | No description available 3.1/O | No description available > hide #1 models > hide #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > close #3 > show #!2 models Drag select of 5 atoms > delete sel > select add #2/B:834@O 1 atom, 1 residue, 1 model selected > select add #2/B:775@O 2 atoms, 2 residues, 1 model selected > select add #2/B:786@O 3 atoms, 3 residues, 1 model selected > select add #2/B:799@O 4 atoms, 4 residues, 1 model selected > select add #2/B:738@O 5 atoms, 5 residues, 1 model selected > select #2 HOH Expected a keyword > select #2/B:HOH 136 atoms, 136 residues, 1 model selected > delete sel > show #1 models > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB > Files/2qjo(NadM).pdb"" 2qjo(NadM).pdb title: Crystal structure of A bifunctional NMN adenylyltransferase/adp ribose pyrophosphatase (nadm) complexed with adprp and nad from synechocystis SP. [more info...] Chain information for 2qjo(NadM).pdb #3 --- Chain | Description | UniProt A B C | bifunctional NMN adenylyltransferase/nudix hydrolase | NADM_SYNY3 1-339 Non-standard residues in 2qjo(NadM).pdb #3 --- APR — adenosine-5-diphosphoribose NAD — nicotinamide-adenine-dinucleotide POP — pyrophosphate 2- SO4 — sulfate ion 26 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select #3/B:285 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 88 atoms, 90 bonds, 10 residues, 1 model selected > select up 2702 atoms, 2775 bonds, 336 residues, 1 model selected > select up 2938 atoms, 2874 bonds, 482 residues, 1 model selected > select up 8622 atoms, 8541 bonds, 1321 residues, 1 model selected > select down 2938 atoms, 2874 bonds, 482 residues, 1 model selected > delete sel > select #3/A:9 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 69 atoms, 71 bonds, 8 residues, 1 model selected > select up 2423 atoms, 2487 bonds, 303 residues, 1 model selected > select up 2432 atoms, 2495 bonds, 304 residues, 1 model selected > delete sel Drag select of 148 atoms, 34 residues, 132 bonds > delete sel > select #1/L #3 4080 atoms, 4024 bonds, 3 pseudobonds, 644 residues, 4 models selected > ui tool show Matchmaker > matchmaker #!3 to #1 ssFraction 0.7122 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.7122 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain L (#1) with 2qjo(NadM).pdb, chain C (#3), sequence alignment score = 419.832 RMSD between 91 pruned atom pairs is 0.910 angstroms; (across all 150 pairs: 17.789) > matchmaker #!3 to #1 ssFraction 0.7122 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.7122 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain L (#1) with 2qjo(NadM).pdb, chain C (#3), sequence alignment score = 419.832 RMSD between 91 pruned atom pairs is 0.910 angstroms; (across all 150 pairs: 17.789) > select clear > select #3/C:177 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 171 atoms, 174 bonds, 20 residues, 1 model selected > select up 1560 atoms, 1605 bonds, 190 residues, 1 model selected > select up 1579 atoms, 1624 bonds, 193 residues, 1 model selected > select down 1560 atoms, 1605 bonds, 190 residues, 1 model selected > delete sel > select #3/B:HOH Nothing selected > select #3:HOH 154 atoms, 154 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 52 atoms, 56 bonds > select up 53 atoms, 56 bonds, 2 residues, 1 model selected > select down 52 atoms, 56 bonds, 2 residues, 1 model selected > delete sel > select clear > select #3/C:603@O7N 1 atom, 1 residue, 1 model selected > delete sel > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 76 atoms, 76 bonds, 10 residues, 1 model selected > select up 284 atoms, 289 bonds, 39 residues, 1 model selected > select up 293 atoms, 297 bonds, 40 residues, 1 model selected > select up 767 atoms, 781 bonds, 101 residues, 1 model selected > delete sel > select #3/C:319 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 55 atoms, 55 bonds, 7 residues, 1 model selected > select up 264 atoms, 273 bonds, 30 residues, 1 model selected > select up 300 atoms, 312 bonds, 31 residues, 1 model selected > select down 264 atoms, 273 bonds, 30 residues, 1 model selected > delete sel > select :RIB 42 atoms, 42 bonds, 3 residues, 1 model selected > delete sel > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB > Files/2qjo(NadM) copy.pdb"" 2qjo(NadM) copy.pdb title: Crystal structure of A bifunctional NMN adenylyltransferase/adp ribose pyrophosphatase (nadm) complexed with adprp and nad from synechocystis SP. [more info...] Chain information for 2qjo(NadM) copy.pdb #4 --- Chain | Description | UniProt A B C | bifunctional NMN adenylyltransferase/nudix hydrolase | NADM_SYNY3 1-339 Non-standard residues in 2qjo(NadM) copy.pdb #4 --- APR — adenosine-5-diphosphoribose NAD — nicotinamide-adenine-dinucleotide POP — pyrophosphate 2- SO4 — sulfate ion 26 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select #4/C:90 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 139 atoms, 140 bonds, 18 residues, 1 model selected > select up 2375 atoms, 2438 bonds, 297 residues, 1 model selected > select up 2384 atoms, 2446 bonds, 298 residues, 1 model selected > select up 2639 atoms, 2711 bonds, 327 residues, 1 model selected > select up 2774 atoms, 2806 bonds, 376 residues, 1 model selected > select up 8622 atoms, 8541 bonds, 1321 residues, 1 model selected > select down 2774 atoms, 2806 bonds, 376 residues, 1 model selected > delete sel > select #4/A:243 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 124 atoms, 123 bonds, 15 residues, 1 model selected > select up 2423 atoms, 2487 bonds, 303 residues, 1 model selected > select up 2432 atoms, 2495 bonds, 304 residues, 1 model selected > select up 2681 atoms, 2754 bonds, 332 residues, 1 model selected > select up 2910 atoms, 2861 bonds, 463 residues, 1 model selected > select up 5848 atoms, 5735 bonds, 945 residues, 1 model selected > select down 2910 atoms, 2861 bonds, 463 residues, 1 model selected > delete sel > select #1/O #4 4233 atoms, 4194 bonds, 649 residues, 2 models selected > ui tool show Matchmaker > matchmaker #!2-4 & sel to #1 & sel ssFraction 0.7122 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.7122 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain O (#1) with 2qjo(NadM) copy.pdb, chain B (#4), sequence alignment score = 367.437 RMSD between 65 pruned atom pairs is 0.736 angstroms; (across all 143 pairs: 15.181) > matchmaker #!2-4 & sel to #1 & sel ssFraction 0.7122 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.7122 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain O (#1) with 2qjo(NadM) copy.pdb, chain B (#4), sequence alignment score = 367.437 RMSD between 65 pruned atom pairs is 0.736 angstroms; (across all 143 pairs: 15.181) > select clear > select #4/B:176 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 171 atoms, 174 bonds, 20 residues, 1 model selected > select up 2702 atoms, 2775 bonds, 336 residues, 1 model selected > select up 2938 atoms, 2874 bonds, 482 residues, 1 model selected > select up 8562 atoms, 8106 bonds, 1648 residues, 4 models selected > select clear > select #4/B:59 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 87 atoms, 87 bonds, 11 residues, 1 model selected > select up 2702 atoms, 2775 bonds, 336 residues, 1 model selected > select up 2938 atoms, 2874 bonds, 482 residues, 1 model selected > select down 2702 atoms, 2775 bonds, 336 residues, 1 model selected > select up 2938 atoms, 2874 bonds, 482 residues, 1 model selected > select down 2702 atoms, 2775 bonds, 336 residues, 1 model selected > delete sel > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 44 atoms, 48 bonds, 1 residue, 1 model selected > delete sel Drag select of 19 atoms, 12 bonds > delete sel > select #4:HOH 137 atoms, 137 residues, 1 model selected > delete sel > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB > Files/2qjo(NadM) copy 2.pdb"" 2qjo(NadM) copy 2.pdb title: Crystal structure of A bifunctional NMN adenylyltransferase/adp ribose pyrophosphatase (nadm) complexed with adprp and nad from synechocystis SP. [more info...] Chain information for 2qjo(NadM) copy 2.pdb #5 --- Chain | Description | UniProt A B C | bifunctional NMN adenylyltransferase/nudix hydrolase | NADM_SYNY3 1-339 Non-standard residues in 2qjo(NadM) copy 2.pdb #5 --- APR — adenosine-5-diphosphoribose NAD — nicotinamide-adenine-dinucleotide POP — pyrophosphate 2- SO4 — sulfate ion 26 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select #5/A:206 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 76 atoms, 76 bonds, 10 residues, 1 model selected > select up 2423 atoms, 2487 bonds, 303 residues, 1 model selected > select up 2432 atoms, 2495 bonds, 304 residues, 1 model selected > select up 2681 atoms, 2754 bonds, 332 residues, 1 model selected > select up 2910 atoms, 2861 bonds, 463 residues, 1 model selected > select up 8622 atoms, 8541 bonds, 1321 residues, 1 model selected > select down 2910 atoms, 2861 bonds, 463 residues, 1 model selected > delete sel > select #5/B:178 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 171 atoms, 174 bonds, 20 residues, 1 model selected > select up 2702 atoms, 2775 bonds, 336 residues, 1 model selected > select up 2938 atoms, 2874 bonds, 482 residues, 1 model selected > delete sel > select #1/M #5 4014 atoms, 4070 bonds, 1 pseudobond, 543 residues, 4 models selected > ui tool show Matchmaker > matchmaker #!5 & sel to #1 & sel ssFraction 0.7122 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.7122 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain M (#1) with 2qjo(NadM) copy 2.pdb, chain C (#5), sequence alignment score = 384.071 RMSD between 83 pruned atom pairs is 0.845 angstroms; (across all 143 pairs: 16.080) > matchmaker #!5 & sel to #1 & sel ssFraction 0.7122 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.7122 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain M (#1) with 2qjo(NadM) copy 2.pdb, chain C (#5), sequence alignment score = 384.071 RMSD between 83 pruned atom pairs is 0.845 angstroms; (across all 143 pairs: 16.080) > select clear > select #5/C:95 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 139 atoms, 140 bonds, 18 residues, 1 model selected > select up 2375 atoms, 2438 bonds, 297 residues, 1 model selected > select up 2384 atoms, 2446 bonds, 298 residues, 1 model selected > select up 2639 atoms, 2711 bonds, 327 residues, 1 model selected > select up 2774 atoms, 2806 bonds, 376 residues, 1 model selected > select down 2639 atoms, 2711 bonds, 327 residues, 1 model selected > select up 2774 atoms, 2806 bonds, 376 residues, 1 model selected > select down 2639 atoms, 2711 bonds, 327 residues, 1 model selected > select up 2774 atoms, 2806 bonds, 376 residues, 1 model selected > select down 2639 atoms, 2711 bonds, 327 residues, 1 model selected > delete sel Drag select of 54 atoms, 56 bonds > delete sel > select #5:HOH 45 atoms, 45 residues, 1 model selected > delete sel > select clear > save /Users/mbanco/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Combined-TK2284-NadM(1).pdb > open /Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Combined-TK2284-NadM(1).pdb Summary of feedback from opening /Users/mbanco/Library/CloudStorage/OneDrive- NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- NEB7-5/Combined-TK2284-NadM(1).pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 SER L 17 LYS L 29 1 13 Start residue of secondary structure not found: HELIX 2 2 VAL L 81 THR L 93 1 13 Start residue of secondary structure not found: HELIX 3 3 ILE L 144 GLU L 146 1 3 Start residue of secondary structure not found: HELIX 4 4 ALA L 147 ASN L 149 1 3 Start residue of secondary structure not found: HELIX 5 5 HIS L 156 ALA L 163 1 8 235 messages similar to the above omitted 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for Combined-TK2284-NadM(1).pdb --- Chain | Description 6.1/L | No description available 6.1/M | No description available 6.1/N | No description available 6.1/O | No description available > hide #1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #6.1 models > show #6.1 models > hide #6.2 models > show #6.2 models > hide #6.3 models > show #6.3 models > hide #6.4 models > show #6.4 models > hide #6.2 models > show #6.2 models > hide #6.2 models > show #6.2 models > hide #6.2 models > show #6.2 models > hide #6.2 models > show #6.2 models > hide #6.2 models > show #6.2 models > close #6 > show #1 models > show #!2 models > show #!3 models > show #!4 models > show #!5 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select #2:HOH 150 atoms, 150 residues, 1 model selected > delete sel > save /Users/mbanco/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Combined-TK2284-NadM(1).pdb > combine #1 #2 #3 #4 #5 name New Remapping chain ID 'B' in 2qjo(NadM).pdb #2 to 'E' Remapping chain ID 'C' in 2qjo(NadM).pdb #3 to 'F' Remapping chain ID 'B' in 2qjo(NadM) copy.pdb #4 to 'G' Remapping chain ID 'C' in 2qjo(NadM) copy 2.pdb #5 to 'H' > hide #1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!6 models > hide #!5 models > show #!6 models > color #6 #7a81ffff > save /Users/mbanco/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Combined-TK2284-NadM(2).pdb models #6 > close #1,6#2-5 > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Manuscript/TK2284 Structure > Manuscript/TK2284-Ribose_Refine_61/ADPR-TK2284-NEB7-5_refine_061.pdb"" Chain information for ADPR-TK2284-NEB7-5_refine_061.pdb #1 --- Chain | Description L | No description available M | No description available N | No description available O | No description available 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > dssp > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/8oxoATP + > Ca/MyModel/Ca_8oxoATP_refine_033-FINAL.pdb"" Chain information for Ca_8oxoATP_refine_033-FINAL.pdb #2 --- Chain | Description A | No description available B | No description available > mmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Ca_8oxoATP_refine_033-FINAL.pdb, chain A (#2) with ADPR- TK2284-NEB7-5_refine_061.pdb, chain O (#1), sequence alignment score = 842.6 RMSD between 156 pruned atom pairs is 0.544 angstroms; (across all 166 pairs: 1.003) > dssp > select add #1 5458 atoms, 5210 bonds, 1018 residues, 1 model selected > show sel atoms > hide #1 models > show #1 models > select subtract #1 Nothing selected > undo > show #1 models > undo > select clear > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB > Files/2qjo(NadM).pdb"" 2qjo(NadM).pdb title: Crystal structure of A bifunctional NMN adenylyltransferase/adp ribose pyrophosphatase (nadm) complexed with adprp and nad from synechocystis SP. [more info...] Chain information for 2qjo(NadM).pdb #3 --- Chain | Description | UniProt A B C | bifunctional NMN adenylyltransferase/nudix hydrolase | NADM_SYNY3 1-339 Non-standard residues in 2qjo(NadM).pdb #3 --- APR — adenosine-5-diphosphoribose NAD — nicotinamide-adenine-dinucleotide POP — pyrophosphate 2- SO4 — sulfate ion 26 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select #3/C:315 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 55 atoms, 55 bonds, 7 residues, 1 model selected > select up 264 atoms, 273 bonds, 30 residues, 1 model selected > select up 323 atoms, 333 bonds, 39 residues, 1 model selected > select up 2639 atoms, 2711 bonds, 327 residues, 1 model selected > select up 2774 atoms, 2806 bonds, 376 residues, 1 model selected > select up 8622 atoms, 8541 bonds, 1321 residues, 1 model selected > select down 2774 atoms, 2806 bonds, 376 residues, 1 model selected > delete sel > select #3/A:208 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 76 atoms, 76 bonds, 10 residues, 1 model selected > select up 2423 atoms, 2487 bonds, 303 residues, 1 model selected > select up 2432 atoms, 2495 bonds, 304 residues, 1 model selected > select up 2681 atoms, 2754 bonds, 332 residues, 1 model selected > select up 2910 atoms, 2861 bonds, 463 residues, 1 model selected > select up 5848 atoms, 5735 bonds, 945 residues, 1 model selected > select down 2910 atoms, 2861 bonds, 463 residues, 1 model selected > delete sel > hide #2 models > select #1/N #3 4211 atoms, 4172 bonds, 648 residues, 2 models selected > ui tool show Matchmaker > matchmaker #!3 & sel to #1 & sel ssFraction 0.7122 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.7122 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain N (#1) with 2qjo(NadM).pdb, chain B (#3), sequence alignment score = 380.183 RMSD between 56 pruned atom pairs is 0.836 angstroms; (across all 146 pairs: 13.312) > matchmaker #!3 & sel to #1 & sel ssFraction 0.7122 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.7122 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ADPR-TK2284-NEB7-5_refine_061.pdb, chain N (#1) with 2qjo(NadM).pdb, chain B (#3), sequence alignment score = 380.183 RMSD between 56 pruned atom pairs is 0.836 angstroms; (across all 146 pairs: 13.312) > show #2 models > hide #1 models > select clear > show #1 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #!3 models > show #!3 models > hide #2 models > show #2 models > hide #!3 models > show #!3 models > hide #2 models > show #1#!3 atoms > show #2 models > hide #2 models > hide #1 models > show #2 models > undo > hide #!3 models > hide #1 models > open /Users/mbanco/Downloads/4JZU.pdb 4JZU.pdb title: Crystal structure of the bacillus subtilis pyrophosphohydrolase bsrpph bound to A non-hydrolysable triphosphorylated dinucleotide RNA (PCP- PGPG) - first guanosine residue In guanosine binding pocket [more info...] Chain information for 4JZU.pdb #4 --- Chain | Description | UniProt A B | RNA pyrophosphohydrolase | YTKD_BACSU 1-158 C | RNA (5'-R(*(GCP)P*G)-3') | Non-standard residues in 4JZU.pdb #4 --- EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES) GCP — phosphomethylphosphonic acid guanylate ester > view #4 clip false > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB > Files/2xsq(NUDT16).pdb"" 2xsq(NUDT16).pdb title: Crystal structure of human nudix motif 16 (NUDT16) In complex with imp and magnesium [more info...] Chain information for 2xsq(NUDT16).pdb #5 --- Chain | Description | UniProt A | U8 snoRNA-decapping enzyme | NUD16_HUMAN 1-195 Non-standard residues in 2xsq(NUDT16).pdb #5 --- CL — chloride ion IMP — inosinic acid MG — magnesium ion 27 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > close #4 > view #5 clip false > close #5 > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB > Files/5bon(NUDT15).pdb"" 5bon(NUDT15).pdb title: Crystal structure of human NUDT15 (MTH2) [more info...] Chain information for 5bon(NUDT15).pdb #4 --- Chain | Description | UniProt A B C D E F G H | probable 8-oxo-DGTP diphosphatase NUDT15 | NUD15_HUMAN 1-164 Non-standard residues in 5bon(NUDT15).pdb #4 --- MG — magnesium ion 58 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > view #4 clip false > select add #4 11037 atoms, 10194 bonds, 166 pseudobonds, 2370 residues, 2 models selected > hide sel cartoons > show sel cartoons > hide sel atoms > close #4 > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structural Comparisons/PDB > Files/3bm4(NUDT5).pdb"" 3bm4(NUDT5).pdb title: Crystal structure of human adp-ribose pyrophosphatase NUDT5 In complex with magnesium and ampcpr [more info...] Chain information for 3bm4(NUDT5).pdb #4 --- Chain | Description | UniProt A B | adp-sugar pyrophosphatase | NUDT5_HUMAN 1-210 Non-standard residues in 3bm4(NUDT5).pdb #4 --- ADV — α-β methylene adp-ribose (ampcpr; {[5-(6-amino- purin-9-yl)-3,4-dihydroxy-tetrahydro-furan-2-ylmethoxy]-hydroxy- phosphorylmethyl}-phosphonic acid mono-(3,4,5-trihydroxy-tetrahydro- furan-2-ylmethyl) ester) MG — magnesium ion > view #4 clip false > hide #!4 models > show #1 models > view #1 clip false > dssp > select #1/A:4@O09 1 atom, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 1 model selected > ui tool show Contacts > contacts sel ignoreHiddenModels true 38 contacts > contacts sel ignoreHiddenModels true 38 contacts > close #5 > ui tool show H-Bonds > hbonds sel restrict cross interModel false intraRes false reveal true 18 hydrogen bonds found > hbonds sel restrict cross interModel false intraRes false reveal true 18 hydrogen bonds found > fetch 3X0S Unknown command: fetch 3X0S > getcrd 3X0S Missing or invalid ""atoms"" argument: invalid atom specifier > ui tool show ""Similar Structures"" You must press the similar structures Search button before you can open matching structures. > foldseek #1/N Not saving entity_poly_seq for non-authoritative sequences Found 383 similar structures to ADPR-TK2284-NEB7-5_refine_061.pdb #1/N in pdb database using foldseek, name fs1 > open 3gz8 Summary of feedback from opening 3gz8 fetched from pdb --- notes | Fetching compressed mmCIF 3gz8 from http://files.rcsb.org/download/3gz8.cif Fetching CCD APR from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/APR/APR.cif 3gz8 title: Cocrystal structure of NUDIX domain of Shewanella oneidensis NrtR complexed with ADP ribose [more info...] Chain information for 3gz8 #5 --- Chain | Description | UniProt A B C D | MutT/nudix family protein | Q8EFJ3_SHEON 1-159 Non-standard residues in 3gz8 #5 --- APR — adenosine-5-diphosphoribose 3gz8 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly Deleted 3 extra chains, 5 C-terminal residues, 2 N-terminal residues, 256 non- polymer residues more than 3.0 Angstroms away. Alignment of 3gz8 chain D to query has RMSD 0.874 using 96 of 139 paired residues within cutoff distance 2.0 > open 3i9x Summary of feedback from opening 3i9x fetched from pdb --- note | Fetching compressed mmCIF 3i9x from http://files.rcsb.org/download/3i9x.cif 3i9x title: Crystal structure of a mutT/nudix family protein from Listeria innocua [more info...] Chain information for 3i9x #6 --- Chain | Description | UniProt A | mutT/nudix family protein | Q92EH0_LISIN 2-177 Non-standard residues in 3i9x #6 --- GOL — glycerol (glycerin; propane-1,2,3-triol) 3i9x mmCIF Assemblies --- 1| author_and_software_defined_assembly Deleted 11 C-terminal residues, 7 non-polymer residues more than 3.0 Angstroms away. Alignment of 3i9x chain A to query has RMSD 0.876 using 85 of 118 paired residues within cutoff distance 2.0 > hide #5 models > open 3cng Summary of feedback from opening 3cng fetched from pdb --- note | Fetching compressed mmCIF 3cng from http://files.rcsb.org/download/3cng.cif 3cng title: Crystal structure of NUDIX hydrolase from Nitrosomonas europaea [more info...] Chain information for 3cng #7 --- Chain | Description | UniProt A B C D | NUDIX hydrolase | Q82VD6_NITEU 1-185 Non-standard residues in 3cng #7 --- CL — chloride ion EDO — 1,2-ethanediol (ethylene glycol) GOL — glycerol (glycerin; propane-1,2,3-triol) NA — sodium ion ZN — zinc ion 3cng mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 23 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 3 extra chains, 20 C-terminal residues, 29 N-terminal residues, 316 non-polymer residues more than 3.0 Angstroms away. Alignment of 3cng chain B to query has RMSD 1.02 using 93 of 125 paired residues within cutoff distance 2.0 > hide #!1 models > hide #6 models > close #6 > close #7 > open 2fml Summary of feedback from opening 2fml fetched from pdb --- note | Fetching compressed mmCIF 2fml from http://files.rcsb.org/download/2fml.cif 2fml title: Crystal structure of MutT/nudix family protein from Enterococcus faecalis [more info...] Chain information for 2fml #6 --- Chain | Description A B | MutT/nudix family protein Non-standard residues in 2fml #6 --- GOL — glycerol (glycerin; propane-1,2,3-triol) 12 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 68 C-terminal residues, 13 N-terminal residues, 201 non-polymer residues more than 3.0 Angstroms away. Alignment of 2fml chain A to query has RMSD 0.614 using 101 of 146 paired residues within cutoff distance 2.0 > close #6 > open 2yyh Summary of feedback from opening 2yyh fetched from pdb --- note | Fetching compressed mmCIF 2yyh from http://files.rcsb.org/download/2yyh.cif 2yyh title: Crystal structure of Nudix family protein from Aquifex aeolicus [more info...] Chain information for 2yyh #6 --- Chain | Description | UniProt A B C D | 8-OXO-dGTPase domain | O67435_AQUAE 1-139 2yyh mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly Deleted 3 extra chains, 6 C-terminal residues, 452 non-polymer residues more than 3.0 Angstroms away. Alignment of 2yyh chain B to query has RMSD 0.759 using 103 of 126 paired residues within cutoff distance 2.0 > show #!1 models > close #6 > open 2qjt Summary of feedback from opening 2qjt fetched from pdb --- note | Fetching compressed mmCIF 2qjt from http://files.rcsb.org/download/2qjt.cif 2qjt title: Crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase complexed with AMP and MN ion from Francisella tularensis [more info...] Chain information for 2qjt #6 --- Chain | Description | UniProt A B | Nicotinamide-nucleotide adenylyltransferase | Q5NHR1_FRATT 1-347 Non-standard residues in 2qjt #6 --- AMP — adenosine monophosphate MN — manganese (II) ion Deleted 1 extra chains, 7 C-terminal residues, 179 N-terminal residues, 332 non-polymer residues more than 3.0 Angstroms away. Alignment of 2qjt chain A to query has RMSD 0.728 using 96 of 131 paired residues within cutoff distance 2.0 > open 2r5w Summary of feedback from opening 2r5w fetched from pdb --- note | Fetching compressed mmCIF 2r5w from http://files.rcsb.org/download/2r5w.cif 2r5w title: Crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase from Francisella tularensis [more info...] Chain information for 2r5w #7 --- Chain | Description | UniProt A B | Nicotinamide-nucleotide adenylyltransferase | Q5NHR1_FRATT 1-347 Non-standard residues in 2r5w #7 --- CL — chloride ion MG — magnesium ion Deleted 1 extra chains, 7 C-terminal residues, 183 N-terminal residues, 360 non-polymer residues more than 3.0 Angstroms away. Alignment of 2r5w chain A to query has RMSD 0.744 using 97 of 137 paired residues within cutoff distance 2.0 > hide #!1 models > hide #!6 models > show #!6 models > hide #!7 models > show #!1 models > show #!7 models > close #7 > open 3i9x 3i9x title: Crystal structure of a mutT/nudix family protein from Listeria innocua [more info...] Chain information for 3i9x #7 --- Chain | Description | UniProt A | mutT/nudix family protein | Q92EH0_LISIN 2-177 Non-standard residues in 3i9x #7 --- GOL — glycerol (glycerin; propane-1,2,3-triol) 3i9x mmCIF Assemblies --- 1| author_and_software_defined_assembly Deleted 11 C-terminal residues, 7 non-polymer residues more than 3.0 Angstroms away. Alignment of 3i9x chain A to query has RMSD 0.876 using 85 of 118 paired residues within cutoff distance 2.0 > hide #!6 models > close #7#6 > open 3cng 3cng title: Crystal structure of NUDIX hydrolase from Nitrosomonas europaea [more info...] Chain information for 3cng #6 --- Chain | Description | UniProt A B C D | NUDIX hydrolase | Q82VD6_NITEU 1-185 Non-standard residues in 3cng #6 --- CL — chloride ion EDO — 1,2-ethanediol (ethylene glycol) GOL — glycerol (glycerin; propane-1,2,3-triol) NA — sodium ion ZN — zinc ion 3cng mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 23 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 3 extra chains, 20 C-terminal residues, 29 N-terminal residues, 316 non-polymer residues more than 3.0 Angstroms away. Alignment of 3cng chain B to query has RMSD 1.02 using 93 of 125 paired residues within cutoff distance 2.0 > close #6 > open 3gz5 Summary of feedback from opening 3gz5 fetched from pdb --- note | Fetching compressed mmCIF 3gz5 from http://files.rcsb.org/download/3gz5.cif 3gz5 title: Crystal structure of Shewanella oneidensis NrtR [more info...] Chain information for 3gz5 #6 --- Chain | Description | UniProt A B | MutT/nudix family protein | Q8EFJ3_SHEON 1-237 Non-standard residues in 3gz5 #6 --- NA — sodium ion Deleted 1 extra chains, 84 C-terminal residues, 2 N-terminal residues, 188 non-polymer residues more than 3.0 Angstroms away. Alignment of 3gz5 chain B to query has RMSD 1.02 using 87 of 116 paired residues within cutoff distance 2.0 > open 2qjo Summary of feedback from opening 2qjo fetched from pdb --- notes | Fetching compressed mmCIF 2qjo from http://files.rcsb.org/download/2qjo.cif Fetching CCD POP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/POP/POP.cif 2qjo title: crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp. [more info...] Chain information for 2qjo #7 --- Chain | Description | UniProt A B C | Bifunctional NMN adenylyltransferase/Nudix hydrolase | NADM_SYNY3 1-339 Non-standard residues in 2qjo #7 --- APR — adenosine-5-diphosphoribose NAD — nicotinamide-adenine-dinucleotide POP — pyrophosphate 2- SO4 — sulfate ion 2qjo mmCIF Assemblies --- 1| author_and_software_defined_assembly 26 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 2 extra chains, 6 C-terminal residues, 179 N-terminal residues, 266 non-polymer residues more than 3.0 Angstroms away. Alignment of 2qjo chain B to query has RMSD 0.971 using 94 of 138 paired residues within cutoff distance 2.0 > close #6-7 > open 3gz5 3gz5 title: Crystal structure of Shewanella oneidensis NrtR [more info...] Chain information for 3gz5 #6 --- Chain | Description | UniProt A B | MutT/nudix family protein | Q8EFJ3_SHEON 1-237 Non-standard residues in 3gz5 #6 --- NA — sodium ion Deleted 1 extra chains, 84 C-terminal residues, 2 N-terminal residues, 188 non-polymer residues more than 3.0 Angstroms away. Alignment of 3gz5 chain B to query has RMSD 1.02 using 87 of 116 paired residues within cutoff distance 2.0 > open 6nci Summary of feedback from opening 6nci fetched from pdb --- notes | Fetching compressed mmCIF 6nci from http://files.rcsb.org/download/6nci.cif Fetching CCD PEG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/PEG/PEG.cif Fetching CCD RB5 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/5/RB5/RB5.cif 6nci title: Crystal structure of CDP-Chase: Vector data collection [more info...] Chain information for 6nci #7 --- Chain | Description | UniProt A B | Phosphohydrolase (MutT/nudix family protein) | Q81EE8_BACCR 1-205 Non-standard residues in 6nci #7 --- PEG — di(hydroxyethyl)ether PO4 — phosphate ion RB5 — D-ribose SO4 — sulfate ion 14 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 14 C-terminal residues, 31 N-terminal residues, 207 non-polymer residues more than 3.0 Angstroms away. Alignment of 6nci chain B to query has RMSD 1.1 using 75 of 137 paired residues within cutoff distance 2.0 > close #6 > hide #!1 models > open 6nch Summary of feedback from opening 6nch fetched from pdb --- note | Fetching compressed mmCIF 6nch from http://files.rcsb.org/download/6nch.cif 6nch title: Crystal structure of CDP-Chase: Raster data collection [more info...] Chain information for 6nch #6 --- Chain | Description | UniProt A B | Phosphohydrolase (MutT/nudix family protein) | Q81EE8_BACCR 1-205 Non-standard residues in 6nch #6 --- PO4 — phosphate ion RB5 — D-ribose SO4 — sulfate ion 42 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 14 C-terminal residues, 31 N-terminal residues, 283 non-polymer residues more than 3.0 Angstroms away. Alignment of 6nch chain B to query has RMSD 1.1 using 74 of 136 paired residues within cutoff distance 2.0 > open 5bs6 Summary of feedback from opening 5bs6 fetched from pdb --- note | Fetching compressed mmCIF 5bs6 from http://files.rcsb.org/download/5bs6.cif 5bs6 title: Apo structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI [more info...] Chain information for 5bs6 #8 --- Chain | Description | UniProt A B C D | transcriptional regulator AraR | Q8AAV8_BACTN 1-225 Non-standard residues in 5bs6 #8 --- EDO — 1,2-ethanediol (ethylene glycol) 5bs6 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly Deleted 3 extra chains, 86 C-terminal residues, 7 N-terminal residues, 227 non-polymer residues more than 3.0 Angstroms away. Alignment of 5bs6 chain B to query has RMSD 1.04 using 87 of 117 paired residues within cutoff distance 2.0 > open 3gg6 Summary of feedback from opening 3gg6 fetched from pdb --- note | Fetching compressed mmCIF 3gg6 from http://files.rcsb.org/download/3gg6.cif 3gg6 title: Crystal structure of the NUDIX domain of human NUDT18 [more info...] Chain information for 3gg6 #9 --- Chain | Description | UniProt A | Nucleoside diphosphate-linked moiety X motif 18 | NUD18_HUMAN 26-179 14 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 13 C-terminal residues, 68 non-polymer residues more than 3.0 Angstroms away. Alignment of 3gg6 chain A to query has RMSD 0.999 using 84 of 124 paired residues within cutoff distance 2.0 > open 6nci 6nci title: Crystal structure of CDP-Chase: Vector data collection [more info...] Chain information for 6nci #10 --- Chain | Description | UniProt A B | Phosphohydrolase (MutT/nudix family protein) | Q81EE8_BACCR 1-205 Non-standard residues in 6nci #10 --- PEG — di(hydroxyethyl)ether PO4 — phosphate ion RB5 — D-ribose SO4 — sulfate ion 14 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 14 C-terminal residues, 31 N-terminal residues, 164 non-polymer residues more than 3.0 Angstroms away. Alignment of 6nci chain A to query has RMSD 0.962 using 66 of 140 paired residues within cutoff distance 2.0 > close #9#6-8 > open 1vcd Summary of feedback from opening 1vcd fetched from pdb --- note | Fetching compressed mmCIF 1vcd from http://files.rcsb.org/download/1vcd.cif 1vcd title: Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase Ndx1 [more info...] Chain information for 1vcd #6 --- Chain | Description | UniProt A B | Ndx1 | Q75UV1_THETH 1-126 Non-standard residues in 1vcd #6 --- GOL — glycerol (glycerin; propane-1,2,3-triol) SO4 — sulfate ion 1vcd mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly Deleted 1 extra chains, 118 non-polymer residues more than 3.0 Angstroms away. Alignment of 1vcd chain A to query has RMSD 0.947 using 76 of 120 paired residues within cutoff distance 2.0 > open 1sz3 Summary of feedback from opening 1sz3 fetched from pdb --- notes | Fetching compressed mmCIF 1sz3 from http://files.rcsb.org/download/1sz3.cif Fetching CCD GNP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GNP/GNP.cif 1sz3 title: Crystal structure of nudix hydrolase DR1025 In complexed with GNP and Mg+2 [more info...] Chain information for 1sz3 #7 --- Chain | Description | UniProt A B | MutT/nudix family protein | Q9RVK2_DEIRA 1-159 Non-standard residues in 1sz3 #7 --- GNP — phosphoaminophosphonic acid-guanylate ester MG — magnesium ion 28 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 9 C-terminal residues, 4 N-terminal residues, 136 non- polymer residues more than 3.0 Angstroms away. Alignment of 1sz3 chain B to query has RMSD 0.912 using 79 of 129 paired residues within cutoff distance 2.0 > hide #6 models > close #6 > close #10 > show #!1 models > open 4dyw Summary of feedback from opening 4dyw fetched from pdb --- note | Fetching compressed mmCIF 4dyw from http://files.rcsb.org/download/4dyw.cif 4dyw title: Crystal structure of MutT NUDIX hydrolase from Burkholderia pseudomallei [more info...] Chain information for 4dyw #6 --- Chain | Description | UniProt A B | MutT/NUDIX family protein | Q3JWU2_BURP1 1-136 4dyw mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| software_defined_assembly Deleted 1 extra chains, 31 non-polymer residues more than 3.0 Angstroms away. Alignment of 4dyw chain A to query has RMSD 1.02 using 92 of 126 paired residues within cutoff distance 2.0 > hide #6 models > hide #!1 models > hide #!7 models > show #6 models > open 3gz6 Summary of feedback from opening 3gz6 fetched from pdb --- note | Fetching compressed mmCIF 3gz6 from http://files.rcsb.org/download/3gz6.cif 3gz6 title: Crystal structure of Shewanella oneidensis NrtR complexed with a 27mer DNA [more info...] Chain information for 3gz6 #8 --- Chain | Description | UniProt A B | MutT/nudix family protein | Q8EFJ3_SHEON 1-237 C | DNA (27-MER) | D | DNA (27-MER) | Non-standard residues in 3gz6 #8 --- NA — sodium ion 36 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 3 extra chains, 87 C-terminal residues, 2 N-terminal residues, 66 non- polymer residues more than 3.0 Angstroms away. Alignment of 3gz6 chain B to query has RMSD 0.928 using 81 of 116 paired residues within cutoff distance 2.0 > open 5bs6 5bs6 title: Apo structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI [more info...] Chain information for 5bs6 #9 --- Chain | Description | UniProt A B C D | transcriptional regulator AraR | Q8AAV8_BACTN 1-225 Non-standard residues in 5bs6 #9 --- EDO — 1,2-ethanediol (ethylene glycol) 5bs6 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly Deleted 3 extra chains, 87 C-terminal residues, 9 N-terminal residues, 226 non-polymer residues more than 3.0 Angstroms away. Alignment of 5bs6 chain D to query has RMSD 1.02 using 83 of 118 paired residues within cutoff distance 2.0 > open 1sjy Summary of feedback from opening 1sjy fetched from pdb --- note | Fetching compressed mmCIF 1sjy from http://files.rcsb.org/download/1sjy.cif 1sjy title: Crystal Structure of NUDIX HYDROLASE DR1025 FROM DEINOCOCCUS RADIODURANS [more info...] Chain information for 1sjy #10 --- Chain | Description | UniProt A | MutT/nudix family protein | Q9RVK2_DEIRA 1-159 1sjy mmCIF Assemblies --- 1| author_defined_assembly 14 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 32 C-terminal residues, 2 N-terminal residues, 45 non-polymer residues more than 3.0 Angstroms away. Alignment of 1sjy chain A to query has RMSD 0.902 using 79 of 113 paired residues within cutoff distance 2.0 > open 3o8s Summary of feedback from opening 3o8s fetched from pdb --- notes | Fetching compressed mmCIF 3o8s from http://files.rcsb.org/download/3o8s.cif Fetching CCD ACT from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/ACT/ACT.cif 3o8s title: Crystal structure of an ADP-ribose pyrophosphatase (SSU98_1448) from STREPTOCOCCUS SUIS 89-1591 at 2.27 A resolution [more info...] Chain information for 3o8s #11 --- Chain | Description | UniProt A | ADP-ribose pyrophosphatase | B9WTJ0_STRSU 1-205 Non-standard residues in 3o8s #11 --- ACT — acetate ion EDO — 1,2-ethanediol (ethylene glycol) 3o8s mmCIF Assemblies --- 1| author_and_software_defined_assembly 2 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 8 C-terminal residues, 20 non-polymer residues more than 3.0 Angstroms away. Alignment of 3o8s chain A to query has RMSD 1.07 using 74 of 118 paired residues within cutoff distance 2.0 > open 3gz5 3gz5 title: Crystal structure of Shewanella oneidensis NrtR [more info...] Chain information for 3gz5 #12 --- Chain | Description | UniProt A B | MutT/nudix family protein | Q8EFJ3_SHEON 1-237 Non-standard residues in 3gz5 #12 --- NA — sodium ion Deleted 1 extra chains, 82 C-terminal residues, 1 N-terminal residues, 176 non-polymer residues more than 3.0 Angstroms away. Alignment of 3gz5 chain A to query has RMSD 0.859 using 81 of 118 paired residues within cutoff distance 2.0 > open 1su2 Summary of feedback from opening 1su2 fetched from pdb --- note | Fetching compressed mmCIF 1su2 from http://files.rcsb.org/download/1su2.cif 1su2 title: Crystal structure of the nudix hydrolase DR1025 In complex with atp [more info...] Chain information for 1su2 #13 --- Chain | Description | UniProt A B | MutT/nudix family protein | Q9RVK2_DEIRA 1-159 Non-standard residues in 1su2 #13 --- ATP — adenosine-5'-triphosphate MG — magnesium ion 35 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 32 C-terminal residues, 3 N-terminal residues, 220 non-polymer residues more than 3.0 Angstroms away. Alignment of 1su2 chain B to query has RMSD 0.905 using 78 of 113 paired residues within cutoff distance 2.0 > close #6#7-12 > open 1soi Summary of feedback from opening 1soi fetched from pdb --- notes | Fetching compressed mmCIF 1soi from http://files.rcsb.org/download/1soi.cif Fetching CCD SM from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/SM/SM.cif 1soi title: Crystal structure of nudix hydrolase DR1025 In complex with Sm+3 [more info...] Chain information for 1soi #6 --- Chain | Description | UniProt A | MutT/nudix family protein | Q9RVK2_DEIRA 1-159 Non-standard residues in 1soi #6 --- SM — samarium (III) ion 1soi mmCIF Assemblies --- 1| author_defined_assembly 7 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 10 C-terminal residues, 2 N-terminal residues, 28 non-polymer residues more than 3.0 Angstroms away. Alignment of 1soi chain A to query has RMSD 0.913 using 78 of 130 paired residues within cutoff distance 2.0 > open 6o3p Summary of feedback from opening 6o3p fetched from pdb --- note | Fetching compressed mmCIF 6o3p from http://files.rcsb.org/download/6o3p.cif 6o3p title: Crystal structure of the catalytic domain of mouse Nudt12 in complex with AMP and 3 Mg2+ ions [more info...] Chain information for 6o3p #7 --- Chain | Description | UniProt A B | Peroxisomal NADH pyrophosphatase NUDT12 | NUD12_MOUSE 126-460 Non-standard residues in 6o3p #7 --- AMP — adenosine monophosphate MG — magnesium ion ZN — zinc ion 29 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 170 N-terminal residues, 238 non-polymer residues more than 3.0 Angstroms away. Alignment of 6o3p chain A to query has RMSD 1.1 using 85 of 122 paired residues within cutoff distance 2.0 > close #6 > close #13 > show #!1 models > select #1/N:37 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #1/O:37 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select clear > open 6m6y Summary of feedback from opening 6m6y fetched from pdb --- note | Fetching compressed mmCIF 6m6y from http://files.rcsb.org/download/6m6y.cif 6m6y title: Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGTP [more info...] Chain information for 6m6y #6 --- Chain | Description | UniProt A | Hydrolase, NUDIX family protein | A0QUZ2_MYCS2 1-322 Non-standard residues in 6m6y #6 --- 8DG — 8-oxo-2'-deoxyguanosine-5'-triphosphate EDO — 1,2-ethanediol (ethylene glycol) MG — magnesium ion PO4 — phosphate ion POP — pyrophosphate 2- 126 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 164 C-terminal residues, 260 non-polymer residues more than 3.0 Angstroms away. Alignment of 6m6y chain A to query has RMSD 0.966 using 97 of 123 paired residues within cutoff distance 2.0 > hide #!7 models > hide #!1 models > open 5gg5 Summary of feedback from opening 5gg5 fetched from pdb --- note | Fetching compressed mmCIF 5gg5 from http://files.rcsb.org/download/5gg5.cif 5gg5 title: Crystal structure of Mycobacterium smegmatis MutT1 [more info...] Chain information for 5gg5 #8 --- Chain | Description | UniProt A | Hydrolase, NUDIX family protein | A0QUZ2_MYCS2 1-322 Non-standard residues in 5gg5 #8 --- EDO — 1,2-ethanediol (ethylene glycol) PEG — di(hydroxyethyl)ether SO4 — sulfate ion 137 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 163 C-terminal residues, 2 N-terminal residues, 216 non-polymer residues more than 3.0 Angstroms away. Alignment of 5gg5 chain A to query has RMSD 1.06 using 93 of 122 paired residues within cutoff distance 2.0 > open 4hvy Summary of feedback from opening 4hvy fetched from pdb --- note | Fetching compressed mmCIF 4hvy from http://files.rcsb.org/download/4hvy.cif 4hvy title: A thermostable variant of human NUDT18 NUDIX domain obtained by Hot Colony Filtration [more info...] Chain information for 4hvy #9 --- Chain | Description | UniProt A | Nucleoside diphosphate-linked moiety X motif 18 | NUD18_HUMAN 26-179 Non-standard residues in 4hvy #9 --- GOL — glycerol (glycerin; propane-1,2,3-triol) MG — magnesium ion NA — sodium ion SO4 — sulfate ion 4hvy mmCIF Assemblies --- 1| author_defined_assembly 2| software_defined_assembly 130 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 7 C-terminal residues, 105 non-polymer residues more than 3.0 Angstroms away. Alignment of 4hvy chain A to query has RMSD 0.987 using 79 of 119 paired residues within cutoff distance 2.0 > close #6 > open 5ggc Summary of feedback from opening 5ggc fetched from pdb --- note | Fetching compressed mmCIF 5ggc from http://files.rcsb.org/download/5ggc.cif 5ggc title: Crystal structure of Mycobacterium smegmatis MutT1 in complex with phosphate and magnesium ions (excess magnesium, I) [more info...] Chain information for 5ggc #6 --- Chain | Description | UniProt A B | Hydrolase, NUDIX family protein | A0QUZ2_MYCS2 1-322 Non-standard residues in 5ggc #6 --- MG — magnesium ion PO4 — phosphate ion 5ggc mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 40 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 163 C-terminal residues, 406 non-polymer residues more than 3.0 Angstroms away. Alignment of 5ggc chain A to query has RMSD 0.984 using 96 of 123 paired residues within cutoff distance 2.0 > open 3i7u Summary of feedback from opening 3i7u fetched from pdb --- notes | Fetching compressed mmCIF 3i7u from http://files.rcsb.org/download/3i7u.cif Fetching CCD PG4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PG4/PG4.cif Fetching CCD PGE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/PGE/PGE.cif 3i7u title: Crystal structure of AP4A hydrolase (aq_158) from Aquifex aeolicus VF5 [more info...] Chain information for 3i7u #10 --- Chain | Description | UniProt A B C D | AP4A hydrolase | O66548_AQUAE 1-134 Non-standard residues in 3i7u #10 --- CL — chloride ion EDO — 1,2-ethanediol (ethylene glycol) PEG — di(hydroxyethyl)ether PG4 — tetraethylene glycol PGE — triethylene glycol TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer) Deleted 3 extra chains, 7 C-terminal residues, 514 non-polymer residues more than 3.0 Angstroms away. Alignment of 3i7u chain B to query has RMSD 0.942 using 98 of 122 paired residues within cutoff distance 2.0 > open 6m72 Summary of feedback from opening 6m72 fetched from pdb --- notes | Fetching compressed mmCIF 6m72 from http://files.rcsb.org/download/6m72.cif Fetching CCD 8GD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/8GD/8GD.cif 6m72 title: Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGDP [more info...] Chain information for 6m72 #11 --- Chain | Description | UniProt A | Hydrolase, NUDIX family protein | A0QUZ2_MYCS2 1-322 Non-standard residues in 6m72 #11 --- 8GD — 2'-deoxy-8-oxoguanosine 5'-(trihydrogen diphosphate) (8-oxo-7,8-dihydro-2'-deoxy-guanosine-5'-diphosphate) MG — magnesium ion POP — pyrophosphate 2- 72 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 164 C-terminal residues, 279 non-polymer residues more than 3.0 Angstroms away. Alignment of 6m72 chain A to query has RMSD 0.967 using 97 of 123 paired residues within cutoff distance 2.0 > open 4hfq Summary of feedback from opening 4hfq fetched from pdb --- note | Fetching compressed mmCIF 4hfq from http://files.rcsb.org/download/4hfq.cif 4hfq title: Crystal structure of UDP-X diphosphatase [more info...] Chain information for 4hfq #12 --- Chain | Description | UniProt A B | MutT/nudix family protein | Q97PF7_STRPN 1-203 Non-standard residues in 4hfq #12 --- EDO — 1,2-ethanediol (ethylene glycol) GOL — glycerol (glycerin; propane-1,2,3-triol) PEG — di(hydroxyethyl)ether PGE — triethylene glycol SO4 — sulfate ion TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer) 209 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 10 C-terminal residues, 51 N-terminal residues, 424 non-polymer residues more than 3.0 Angstroms away. Alignment of 4hfq chain B to query has RMSD 0.944 using 72 of 132 paired residues within cutoff distance 2.0 > close #10,12#8-9,11 > open 3id9 Summary of feedback from opening 3id9 fetched from pdb --- note | Fetching compressed mmCIF 3id9 from http://files.rcsb.org/download/3id9.cif 3id9 title: Crystal structure of a MutT/NUDIX family protein from Bacillus thuringiensis [more info...] Chain information for 3id9 #8 --- Chain | Description A B | MutT/NUDIX family protein Non-standard residues in 3id9 #8 --- CL — chloride ion SO4 — sulfate ion Deleted 1 extra chains, 9 C-terminal residues, 96 non-polymer residues more than 3.0 Angstroms away. Alignment of 3id9 chain A to query has RMSD 0.995 using 77 of 115 paired residues within cutoff distance 2.0 > open 6o3p 6o3p title: Crystal structure of the catalytic domain of mouse Nudt12 in complex with AMP and 3 Mg2+ ions [more info...] Chain information for 6o3p #9 --- Chain | Description | UniProt A B | Peroxisomal NADH pyrophosphatase NUDT12 | NUD12_MOUSE 126-460 Non-standard residues in 6o3p #9 --- AMP — adenosine monophosphate MG — magnesium ion ZN — zinc ion 29 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 2 C-terminal residues, 182 N-terminal residues, 243 non-polymer residues more than 3.0 Angstroms away. Alignment of 6o3p chain B to query has RMSD 1.14 using 86 of 125 paired residues within cutoff distance 2.0 > hide #!8 models > hide #!9 models > show #!9 models > hide #!6 models > open 3id9 3id9 title: Crystal structure of a MutT/NUDIX family protein from Bacillus thuringiensis [more info...] Chain information for 3id9 #10 --- Chain | Description A B | MutT/NUDIX family protein Non-standard residues in 3id9 #10 --- CL — chloride ion SO4 — sulfate ion Deleted 1 extra chains, 12 C-terminal residues, 88 non-polymer residues more than 3.0 Angstroms away. Alignment of 3id9 chain B to query has RMSD 0.993 using 73 of 115 paired residues within cutoff distance 2.0 > open 3smd Summary of feedback from opening 3smd fetched from pdb --- note | Fetching compressed mmCIF 3smd from http://files.rcsb.org/download/3smd.cif 3smd title: Crystal structure of a mut/nudix family protein from bacillus thuringiensis [more info...] Chain information for 3smd #11 --- Chain | Description A | MutT/NUDIX family protein 3smd mmCIF Assemblies --- 1| author_defined_assembly 2| software_defined_assembly Deleted 2 C-terminal residues, 3 N-terminal residues, 45 non-polymer residues more than 3.0 Angstroms away. Alignment of 3smd chain A to query has RMSD 0.882 using 76 of 121 paired residues within cutoff distance 2.0 > open 6scx Summary of feedback from opening 6scx fetched from pdb --- notes | Fetching compressed mmCIF 6scx from http://files.rcsb.org/download/6scx.cif Fetching CCD CD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/CD/CD.cif Fetching CCD MGP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/MGP/MGP.cif 6scx title: Crystal structure of the catalytic domain of human NUDT12 in complex with 7-methyl-guanosine-5'-triphosphate [more info...] Chain information for 6scx #12 --- Chain | Description | UniProt A B C | Peroxisomal NADH pyrophosphatase NUDT12 | NUD12_HUMAN 111-462 Non-standard residues in 6scx #12 --- CD — cadmium ion MGP — 7-methyl-guanosine-5'-triphosphate 6scx mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 99 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 2 extra chains, 6 C-terminal residues, 182 N-terminal residues, 14 non-polymer residues more than 3.0 Angstroms away. Alignment of 6scx chain A to query has RMSD 1.09 using 84 of 122 paired residues within cutoff distance 2.0 > hide #!9 models > hide #!10 models > hide #!11 models > show #!1 models > open 5isy Summary of feedback from opening 5isy fetched from pdb --- note | Fetching compressed mmCIF 5isy from http://files.rcsb.org/download/5isy.cif 5isy title: Crystal structure of Nudix family protein with NAD [more info...] Chain information for 5isy #13 --- Chain | Description | UniProt A C | NADH pyrophosphatase | NUDC_ECOLI 1-257 Non-standard residues in 5isy #13 --- NAD — nicotinamide-adenine-dinucleotide ZN — zinc ion 6 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 70 N-terminal residues, 159 non-polymer residues more than 3.0 Angstroms away. Alignment of 5isy chain C to query has RMSD 0.964 using 83 of 145 paired residues within cutoff distance 2.0 > hide #!12 models > open 5xd2 Summary of feedback from opening 5xd2 fetched from pdb --- notes | Fetching compressed mmCIF 5xd2 from http://files.rcsb.org/download/5xd2.cif Fetching CCD 5FA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/5FA/5FA.cif 5xd2 title: Crystal structure of Mycobacterium smegmatis MutT1 in complex with Ap5A, ATP and manganese [more info...] Chain information for 5xd2 #14 --- Chain | Description | UniProt A | NUDIX family protein | A0QUZ2_MYCS2 1-322 Non-standard residues in 5xd2 #14 --- 5FA — adenosine-5'-pentaphosphate ATP — adenosine-5'-triphosphate GOL — glycerol (glycerin; propane-1,2,3-triol) MN — manganese (II) ion 44 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 168 C-terminal residues, 205 non-polymer residues more than 3.0 Angstroms away. Alignment of 5xd2 chain A to query has RMSD 0.953 using 89 of 120 paired residues within cutoff distance 2.0 > hide #!13 models > hide #!1 models > open 5deq Summary of feedback from opening 5deq fetched from pdb --- notes | Fetching compressed mmCIF 5deq from http://files.rcsb.org/download/5deq.cif Fetching CCD ARA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/ARA/ARA.cif 5deq title: Crystal structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI in complex with L-arabinose [more info...] Chain information for 5deq #15 --- Chain | Description | UniProt A B | TRANSCRIPTIONAL REGULATOR AraR | Q8AAV8_BACTN 1-225 Non-standard residues in 5deq #15 --- ARA — alpha-L-arabinopyranose (alpha-L-arabinose; L-arabinose; arabinose) FMT — formic acid SO4 — sulfate ion 74 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 76 C-terminal residues, 5 N-terminal residues, 184 non-polymer residues more than 3.0 Angstroms away. Alignment of 5deq chain A to query has RMSD 0.953 using 83 of 121 paired residues within cutoff distance 2.0 > hide #!14 models > open 2gb5 Summary of feedback from opening 2gb5 fetched from pdb --- note | Fetching compressed mmCIF 2gb5 from http://files.rcsb.org/download/2gb5.cif 2gb5 title: Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli K12 at 2.30 A resolution [more info...] Chain information for 2gb5 #16 --- Chain | Description | UniProt A B | NADH pyrophosphatase | NUDC_ECOLI 1-257 Non-standard residues in 2gb5 #16 --- ZN — zinc ion 45 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 8 C-terminal residues, 124 N-terminal residues, 206 non-polymer residues more than 3.0 Angstroms away. Alignment of 2gb5 chain B to query has RMSD 0.961 using 86 of 123 paired residues within cutoff distance 2.0 > open 5gg7 Summary of feedback from opening 5gg7 fetched from pdb --- notes | Fetching compressed mmCIF 5gg7 from http://files.rcsb.org/download/5gg7.cif Fetching CCD 8OG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/8OG/8OG.cif 5gg7 title: Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGTP, 8-oxo-dGMP and pyrophosphate (I) [more info...] Chain information for 5gg7 #17 --- Chain | Description | UniProt A B | Hydrolase, NUDIX family protein | A0QUZ2_MYCS2 1-322 Non-standard residues in 5gg7 #17 --- 8DG — 8-oxo-2'-deoxyguanosine-5'-triphosphate 8OG — 8-oxo-2'-deoxy-guanosine-5'-monophosphate (8-oxo-7,8-dihydro-2'-deoxy- guanosine-5'-monophosphate) MG — magnesium ion POP — pyrophosphate 2- 5gg7 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 76 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 164 C-terminal residues, 546 non-polymer residues more than 3.0 Angstroms away. Alignment of 5gg7 chain A to query has RMSD 0.979 using 93 of 123 paired residues within cutoff distance 2.0 > open 3f13 Summary of feedback from opening 3f13 fetched from pdb --- note | Fetching compressed mmCIF 3f13 from http://files.rcsb.org/download/3f13.cif 3f13 title: Crystal structure of putative nudix hydrolase family member from Chromobacterium violaceum [more info...] Chain information for 3f13 #18 --- Chain | Description | UniProt A B | putative nudix hydrolase family member | Q7NWQ3_CHRVO 4-156 20 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 33 C-terminal residues, 1 N-terminal residues, 142 non-polymer residues more than 3.0 Angstroms away. Alignment of 3f13 chain B to query has RMSD 1.08 using 76 of 111 paired residues within cutoff distance 2.0 > hide #!16 models > hide #!15 models > hide #!17 models > show #!17 models > show #!7 models > show #!10 models > show #!9 models > hide #!10 models > close #10-18 > hide #!7 models > hide #!9 models > open 5gp0 Summary of feedback from opening 5gp0 fetched from pdb --- notes | Fetching compressed mmCIF 5gp0 from http://files.rcsb.org/download/5gp0.cif Fetching CCD GPP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GPP/GPP.cif 5gp0 title: Crystal structure of geraniol-NUDX1 complex [more info...] Chain information for 5gp0 #10 --- Chain | Description | UniProt A E F I | Nudix hydrolase 1 | NUDT1_ARATH 1-147 7-153 Non-standard residues in 5gp0 #10 --- GOL — glycerol (glycerin; propane-1,2,3-triol) GPP — geranyl diphosphate 5gp0 mmCIF Assemblies --- 1| author_defined_assembly 2| software_defined_assembly 3| software_defined_assembly 122 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 3 extra chains, 17 C-terminal residues, 593 non-polymer residues more than 3.0 Angstroms away. Alignment of 5gp0 chain I to query has RMSD 1.09 using 83 of 114 paired residues within cutoff distance 2.0 > open 3grn Summary of feedback from opening 3grn fetched from pdb --- note | Fetching compressed mmCIF 3grn from http://files.rcsb.org/download/3grn.cif 3grn title: CRYSTAL STRUCTURE OF MUTT PROTEIN FROM Methanosarcina mazei Go1 [more info...] Chain information for 3grn #11 --- Chain | Description | UniProt A B | MutT related protein | Q8PYE2_METMA 3-145 Non-standard residues in 3grn #11 --- GOL — glycerol (glycerin; propane-1,2,3-triol) 3grn mmCIF Assemblies --- 1| author_defined_assembly 2| author_and_software_defined_assembly 68 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 8 C-terminal residues, 111 non-polymer residues more than 3.0 Angstroms away. Alignment of 3grn chain A to query has RMSD 1.11 using 67 of 123 paired residues within cutoff distance 2.0 > open 6dt3 Summary of feedback from opening 6dt3 fetched from pdb --- notes | Fetching compressed mmCIF 6dt3 from http://files.rcsb.org/download/6dt3.cif Fetching CCD EPE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/EPE/EPE.cif 6dt3 title: 1.2 Angstrom Resolution Crystal Structure of Nucleoside Triphosphatase NudI from Klebsiella pneumoniae in Complex with HEPES [more info...] Chain information for 6dt3 #12 --- Chain | Description | UniProt A B | Nucleoside triphosphatase NudI | A0A1W1Q5B1_KLEPN 1-141 Non-standard residues in 6dt3 #12 --- EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES) 275 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 5 C-terminal residues, 3 N-terminal residues, 222 non- polymer residues more than 3.0 Angstroms away. Alignment of 6dt3 chain A to query has RMSD 1.11 using 79 of 122 paired residues within cutoff distance 2.0 > open 5iw5 Summary of feedback from opening 5iw5 fetched from pdb --- notes | Fetching compressed mmCIF 5iw5 from http://files.rcsb.org/download/5iw5.cif Fetching CCD NMN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/NMN/NMN.cif 5iw5 title: Crystal structure of E. coli NudC in complex with NMN [more info...] Chain information for 5iw5 #13 --- Chain | Description | UniProt A B | NADH pyrophosphatase | D6JHV3_ECOLX 1-257 Non-standard residues in 5iw5 #13 --- NMN — β-nicotinamide ribose monophosphate (nicotinamide mononucleotide) ZN — zinc ion 5iw5 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly Deleted 1 extra chains, 10 C-terminal residues, 116 N-terminal residues, 96 non-polymer residues more than 3.0 Angstroms away. Alignment of 5iw5 chain A to query has RMSD 1.16 using 86 of 122 paired residues within cutoff distance 2.0 > close #10-12#13 > open 1vc9 Summary of feedback from opening 1vc9 fetched from pdb --- note | Fetching compressed mmCIF 1vc9 from http://files.rcsb.org/download/1vc9.cif 1vc9 title: Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase E50Q mutant-Mg2+-ATP complex [more info...] Chain information for 1vc9 #10 --- Chain | Description | UniProt A B | Ndx1 | Q75UV1_THETH 1-126 Non-standard residues in 1vc9 #10 --- ATP — adenosine-5'-triphosphate MG — magnesium ion 1vc9 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly Deleted 1 extra chains, 5 C-terminal residues, 74 non-polymer residues more than 3.0 Angstroms away. Alignment of 1vc9 chain B to query has RMSD 1.08 using 84 of 118 paired residues within cutoff distance 2.0 > open 6t5j Summary of feedback from opening 6t5j fetched from pdb --- notes | Fetching compressed mmCIF 6t5j from http://files.rcsb.org/download/6t5j.cif Fetching CCD MKB from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/MKB/MKB.cif 6t5j title: Structure of NUDT15 in complex with inhibitor TH1760 [more info...] Chain information for 6t5j #11 --- Chain | Description | UniProt A B | Probable 8-oxo-dGTP diphosphatase NUDT15 | NUD15_HUMAN 1-164 Non-standard residues in 6t5j #11 --- CL — chloride ion MG — magnesium ion MKB — 6-[4-(1~{H}-indol-5-ylcarbonyl)piperazin-1-yl]sulfonyl-3~{H}-1,3-benzoxazol-2-one 27 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 34 C-terminal residues, 342 non-polymer residues more than 3.0 Angstroms away. Alignment of 6t5j chain B to query has RMSD 1.16 using 75 of 110 paired residues within cutoff distance 2.0 > open 3n77 Summary of feedback from opening 3n77 fetched from pdb --- note | Fetching compressed mmCIF 3n77 from http://files.rcsb.org/download/3n77.cif 3n77 title: Crystal structure of Idp01880, putative NTP pyrophosphohydrolase of Salmonella typhimurium LT2 [more info...] Chain information for 3n77 #12 --- Chain | Description | UniProt A B | Nucleoside triphosphatase nudI | NUDI_SALTY 1-141 3n77 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_and_software_defined_assembly 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 5 C-terminal residues, 131 non-polymer residues more than 3.0 Angstroms away. Alignment of 3n77 chain A to query has RMSD 1.15 using 80 of 123 paired residues within cutoff distance 2.0 > open 3dku Summary of feedback from opening 3dku fetched from pdb --- note | Fetching compressed mmCIF 3dku from http://files.rcsb.org/download/3dku.cif 3dku title: Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1 [more info...] Chain information for 3dku #13 --- Chain | Description | UniProt A B C D E F G H | Putative phosphohydrolase | A1AA28_ECOK1 1-153 3dku mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly 5| author_defined_assembly 6| author_defined_assembly 7| author_defined_assembly 8| author_defined_assembly Deleted 7 extra chains, 19 C-terminal residues, 142 non-polymer residues more than 3.0 Angstroms away. Alignment of 3dku chain H to query has RMSD 0.86 using 74 of 121 paired residues within cutoff distance 2.0 > open 6scx 6scx title: Crystal structure of the catalytic domain of human NUDT12 in complex with 7-methyl-guanosine-5'-triphosphate [more info...] Chain information for 6scx #14 --- Chain | Description | UniProt A B C | Peroxisomal NADH pyrophosphatase NUDT12 | NUD12_HUMAN 111-462 Non-standard residues in 6scx #14 --- CD — cadmium ion MGP — 7-methyl-guanosine-5'-triphosphate 6scx mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 99 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 2 extra chains, 6 C-terminal residues, 179 N-terminal residues, 14 non-polymer residues more than 3.0 Angstroms away. Alignment of 6scx chain B to query has RMSD 1.08 using 83 of 122 paired residues within cutoff distance 2.0 > close #12-13#10-11 > open 3oga Summary of feedback from opening 3oga fetched from pdb --- notes | Fetching compressed mmCIF 3oga from http://files.rcsb.org/download/3oga.cif Fetching CCD BME from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/BME/BME.cif 3oga title: 1.75 Angstrom resolution crystal structure of a putative NTP pyrophosphohydrolase (yfaO) from Salmonella typhimurium LT2 [more info...] Chain information for 3oga #10 --- Chain | Description | UniProt A B | Nucleoside triphosphatase nudI | NUDI_SALTY 1-141 Non-standard residues in 3oga #10 --- BME — β-mercaptoethanol PO4 — phosphate ion 183 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 5 C-terminal residues, 175 non-polymer residues more than 3.0 Angstroms away. Alignment of 3oga chain B to query has RMSD 1.11 using 82 of 116 paired residues within cutoff distance 2.0 > open 5isy 5isy title: Crystal structure of Nudix family protein with NAD [more info...] Chain information for 5isy #11 --- Chain | Description | UniProt A C | NADH pyrophosphatase | NUDC_ECOLI 1-257 Non-standard residues in 5isy #11 --- NAD — nicotinamide-adenine-dinucleotide ZN — zinc ion 6 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 7 C-terminal residues, 118 N-terminal residues, 170 non-polymer residues more than 3.0 Angstroms away. Alignment of 5isy chain A to query has RMSD 0.931 using 81 of 122 paired residues within cutoff distance 2.0 > open 3ees Summary of feedback from opening 3ees fetched from pdb --- note | Fetching compressed mmCIF 3ees from http://files.rcsb.org/download/3ees.cif 3ees title: Structure of the RNA pyrophosphohydrolase BdRppH [more info...] Chain information for 3ees #12 --- Chain | Description | UniProt A B | Probable pyrophosphohydrolase | Q6MPX4_BDEBA 1-153 Deleted 1 extra chains, 9 C-terminal residues, 69 non-polymer residues more than 3.0 Angstroms away. Alignment of 3ees chain B to query has RMSD 1.04 using 78 of 118 paired residues within cutoff distance 2.0 > open 1rya Summary of feedback from opening 1rya fetched from pdb --- notes | Fetching compressed mmCIF 1rya from http://files.rcsb.org/download/1rya.cif Fetching CCD GDP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GDP/GDP.cif 1rya title: Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG [more info...] Chain information for 1rya #13 --- Chain | Description | UniProt A B | GDP-mannose mannosyl hydrolase | NUDD_ECOLI 1-160 Non-standard residues in 1rya #13 --- CL — chloride ion GDP — guanosine-5'-diphosphate MG — magnesium ion TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer) Deleted 1 extra chains, 11 C-terminal residues, 6 N-terminal residues, 563 non-polymer residues more than 3.0 Angstroms away. Alignment of 1rya chain B to query has RMSD 0.966 using 65 of 130 paired residues within cutoff distance 2.0 > hide #!10 models > hide #!11 models > hide #!12 models > hide #!13 models > open 1rya 1rya title: Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG [more info...] Chain information for 1rya #15 --- Chain | Description | UniProt A B | GDP-mannose mannosyl hydrolase | NUDD_ECOLI 1-160 Non-standard residues in 1rya #15 --- CL — chloride ion GDP — guanosine-5'-diphosphate MG — magnesium ion TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer) Deleted 1 extra chains, 11 C-terminal residues, 6 N-terminal residues, 563 non-polymer residues more than 3.0 Angstroms away. Alignment of 1rya chain B to query has RMSD 0.966 using 65 of 130 paired residues within cutoff distance 2.0 > hide #!14 models > open 5wy6 Summary of feedback from opening 5wy6 fetched from pdb --- note | Fetching compressed mmCIF 5wy6 from http://files.rcsb.org/download/5wy6.cif 5wy6 title: Crystal structure of AtNUDX1 (E56A) [more info...] Chain information for 5wy6 #16 --- Chain | Description | UniProt A E | Nudix hydrolase 1 | NUDT1_ARATH 1-147 Non-standard residues in 5wy6 #16 --- GOL — glycerol (glycerin; propane-1,2,3-triol) PEG — di(hydroxyethyl)ether SO4 — sulfate ion 12 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 16 C-terminal residues, 120 non-polymer residues more than 3.0 Angstroms away. Alignment of 5wy6 chain A to query has RMSD 1.09 using 83 of 114 paired residues within cutoff distance 2.0 > open 4zbp Summary of feedback from opening 4zbp fetched from pdb --- notes | Fetching compressed mmCIF 4zbp from http://files.rcsb.org/download/4zbp.cif Fetching CCD ADV from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/V/ADV/ADV.cif 4zbp title: Crystal structure of the AMPCPR-bound AtNUDT7 [more info...] Chain information for 4zbp #17 --- Chain | Description | UniProt A B C | Nudix hydrolase 7 | NUDT7_ARATH 1-282 Non-standard residues in 4zbp #17 --- ADV — α-β methylene adp-ribose (ampcpr; {[5-(6-amino- purin-9-yl)-3,4-dihydroxy-tetrahydro-furan-2-ylmethoxy]-hydroxy- phosphorylmethyl}-phosphonic acid mono-(3,4,5-trihydroxy-tetrahydro- furan-2-ylmethyl) ester) SO4 — sulfate ion 4zbp mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly Deleted 2 extra chains, 62 C-terminal residues, 89 N-terminal residues, 86 non-polymer residues more than 3.0 Angstroms away. Alignment of 4zbp chain B to query has RMSD 1.06 using 83 of 113 paired residues within cutoff distance 2.0 > open 3oga 3oga title: 1.75 Angstrom resolution crystal structure of a putative NTP pyrophosphohydrolase (yfaO) from Salmonella typhimurium LT2 [more info...] Chain information for 3oga #18 --- Chain | Description | UniProt A B | Nucleoside triphosphatase nudI | NUDI_SALTY 1-141 Non-standard residues in 3oga #18 --- BME — β-mercaptoethanol PO4 — phosphate ion 183 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 5 C-terminal residues, 149 non-polymer residues more than 3.0 Angstroms away. Alignment of 3oga chain A to query has RMSD 1.12 using 83 of 120 paired residues within cutoff distance 2.0 > similarstructures sequences > open 8dwe Summary of feedback from opening 8dwe fetched from pdb --- warnings | Atom HO5' is not in the residue template for DA /B:1 Atom HO5' is not in the residue template for DA /E:1 notes | Fetching compressed mmCIF 8dwe from http://files.rcsb.org/download/8dwe.cif Fetching CCD PRN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/PRN/PRN.cif Fetching CCD SF4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SF4/SF4.cif 8dwe title: Adenine glycosylase MutY variant E43Q in complex with DNA containing d(8-oxo-G) paired with substrate purine [more info...] Chain information for 8dwe #19 --- Chain | Description | UniProt A D | Adenine DNA glycosylase | MUTY_GEOSE 1-365 B E | DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3') | C F | DNA (5'-D(*TP*GP*TP*CP*CP*AP*(PRN)P*GP*TP*CP*T)-3') | Non-standard residues in 8dwe #19 --- CA — calcium ion EDO — 1,2-ethanediol (ethylene glycol) SF4 — iron/sulfur cluster TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer) 8dwe mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly Deleted 5 extra chains, 6 C-terminal residues, 206 N-terminal residues, 190 non-polymer residues more than 3.0 Angstroms away. Alignment of 8dwe chain D to query has RMSD 0.984 using 55 of 136 paired residues within cutoff distance 2.0 > open 3x0o Summary of feedback from opening 3x0o fetched from pdb --- note | Fetching compressed mmCIF 3x0o from http://files.rcsb.org/download/3x0o.cif 3x0o title: ADP ribose pyrophosphatase from Thermus thermophilus HB8 in ESMM-state at reaction time of 10 min [more info...] Chain information for 3x0o #20 --- Chain | Description | UniProt A | ADP-ribose pyrophosphatase | Q5SKW5_THET8 1-170 Non-standard residues in 3x0o #20 --- AR6 — [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate (Adenosine-5-Diphosphoribose) GOL — glycerol (glycerin; propane-1,2,3-triol) MN — manganese (II) ion SO4 — sulfate ion 3x0o mmCIF Assemblies --- 1| author_and_software_defined_assembly 144 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 9 C-terminal residues, 14 N-terminal residues, 60 non-polymer residues more than 3.0 Angstroms away. Alignment of 3x0o chain A to query has RMSD 0.936 using 60 of 118 paired residues within cutoff distance 2.0 > show #!1 models > hide #!15 models > hide #16 models > hide #!17 models > hide #!18 models > hide #!19 models > open 1viq Summary of feedback from opening 1viq fetched from pdb --- note | Fetching compressed mmCIF 1viq from http://files.rcsb.org/download/1viq.cif 1viq title: Crystal structure of putative ADP ribose pyrophosphatase [more info...] Chain information for 1viq #21 --- Chain | Description | UniProt A B C | ADP-ribose pyrophosphatase | ADPP_ECOLI 1-208 1viq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| software_defined_assembly 4| software_defined_assembly 5| software_defined_assembly 7 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 2 extra chains, 32 C-terminal residues, 45 N-terminal residues, 205 non-polymer residues more than 3.0 Angstroms away. Alignment of 1viq chain B to query has RMSD 0.89 using 62 of 109 paired residues within cutoff distance 2.0 > open 1khz Summary of feedback from opening 1khz fetched from pdb --- note | Fetching compressed mmCIF 1khz from http://files.rcsb.org/download/1khz.cif 1khz title: Structure of the ADPR-ase in complex with AMPCPR and Mg [more info...] Chain information for 1khz #22 --- Chain | Description | UniProt A B | ADP-ribose pyrophosphatase | ADPP_ECOLI 1-209 Non-standard residues in 1khz #22 --- ADV — α-β methylene adp-ribose (ampcpr; {[5-(6-amino- purin-9-yl)-3,4-dihydroxy-tetrahydro-furan-2-ylmethoxy]-hydroxy- phosphorylmethyl}-phosphonic acid mono-(3,4,5-trihydroxy-tetrahydro- furan-2-ylmethyl) ester) CL — chloride ion MG — magnesium ion Deleted 1 extra chains, 32 C-terminal residues, 38 N-terminal residues, 155 non-polymer residues more than 3.0 Angstroms away. Alignment of 1khz chain B to query has RMSD 0.871 using 59 of 110 paired residues within cutoff distance 2.0 > open 1khz 1khz title: Structure of the ADPR-ase in complex with AMPCPR and Mg [more info...] Chain information for 1khz #23 --- Chain | Description | UniProt A B | ADP-ribose pyrophosphatase | ADPP_ECOLI 1-209 Non-standard residues in 1khz #23 --- ADV — α-β methylene adp-ribose (ampcpr; {[5-(6-amino- purin-9-yl)-3,4-dihydroxy-tetrahydro-furan-2-ylmethoxy]-hydroxy- phosphorylmethyl}-phosphonic acid mono-(3,4,5-trihydroxy-tetrahydro- furan-2-ylmethyl) ester) CL — chloride ion MG — magnesium ion Deleted 1 extra chains, 32 C-terminal residues, 38 N-terminal residues, 155 non-polymer residues more than 3.0 Angstroms away. Alignment of 1khz chain B to query has RMSD 0.871 using 59 of 110 paired residues within cutoff distance 2.0 > open 1mqw Summary of feedback from opening 1mqw fetched from pdb --- note | Fetching compressed mmCIF 1mqw from http://files.rcsb.org/download/1mqw.cif 1mqw title: Structure of the MT-ADPRase in complex with three Mn2+ ions and AMPCPR, a Nudix enzyme [more info...] Chain information for 1mqw #24 --- Chain | Description | UniProt A | ADPR pyrophosphatase | O33199_MYCTU 1-207 Non-standard residues in 1mqw #24 --- ADV — α-β methylene adp-ribose (ampcpr; {[5-(6-amino- purin-9-yl)-3,4-dihydroxy-tetrahydro-furan-2-ylmethoxy]-hydroxy- phosphorylmethyl}-phosphonic acid mono-(3,4,5-trihydroxy-tetrahydro- furan-2-ylmethyl) ester) MN — manganese (II) ion 1mqw mmCIF Assemblies --- 1| author_and_software_defined_assembly Deleted 38 C-terminal residues, 40 N-terminal residues, 23 non-polymer residues more than 3.0 Angstroms away. Alignment of 1mqw chain A to query has RMSD 0.86 using 64 of 112 paired residues within cutoff distance 2.0 > hide #!20 models > hide #!21 models > hide #!22 models > hide #!23 models > close #16#10-15,17-24 > open 7ef8 Summary of feedback from opening 7ef8 fetched from pdb --- notes | Fetching compressed mmCIF 7ef8 from http://files.rcsb.org/download/7ef8.cif Fetching CCD 3DR from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/3DR/3DR.cif 7ef8 title: Crystal structure of mouse MUTYH in complex with DNA containing AP site analogue:8-oxoG (Form I) [more info...] Chain information for 7ef8 #10 --- Chain | Description | UniProt A | Adenine DNA glycosylase | MUTYH_MOUSE 35-487 B | DNA (5'-D(*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)-3') | C | DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3') | Non-standard residues in 7ef8 #10 --- SF4 — iron/sulfur cluster SO4 — sulfate ion ZN — zinc ion 21 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 2 extra chains, 6 C-terminal residues, 257 N-terminal residues, 66 non-polymer residues more than 3.0 Angstroms away. Alignment of 7ef8 chain A to query has RMSD 1.08 using 54 of 123 paired residues within cutoff distance 2.0 > open 5j3t 5j3t title: Crystal structure of S. pombe Dcp2:Dcp1:Edc1 mRNA decapping complex [more info...] Chain information for 5j3t #11 --- Chain | Description | UniProt A | mRNA-decapping enzyme subunit 1 | DCP1_SCHPO 1-127 B | mRNA decapping complex subunit 2 | DCP2_SCHPO 1-242 C | Edc1 | YAQ9_SCHPO 155-180 Non-standard residues in 5j3t #11 --- FMT — formic acid MG — magnesium ion 105 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 2 extra chains, 26 C-terminal residues, 57 N-terminal residues, 152 non-polymer residues more than 3.0 Angstroms away. Alignment of 5j3t chain B to query has RMSD 0.915 using 63 of 124 paired residues within cutoff distance 2.0 > open 1mk1 Summary of feedback from opening 1mk1 fetched from pdb --- note | Fetching compressed mmCIF 1mk1 from http://files.rcsb.org/download/1mk1.cif 1mk1 title: Structure of the MT-ADPRase in complex with ADPR, a Nudix enzyme [more info...] Chain information for 1mk1 #12 --- Chain | Description | UniProt A | ADPR pyrophosphatase | O33199_MYCTU 1-207 Non-standard residues in 1mk1 #12 --- APR — adenosine-5-diphosphoribose 1mk1 mmCIF Assemblies --- 1| author_and_software_defined_assembly Deleted 41 C-terminal residues, 34 N-terminal residues, 53 non-polymer residues more than 3.0 Angstroms away. Alignment of 1mk1 chain A to query has RMSD 0.939 using 70 of 107 paired residues within cutoff distance 2.0 > hide #!10 models > hide #!11 models > open 5c7q Summary of feedback from opening 5c7q fetched from pdb --- notes | Fetching compressed mmCIF 5c7q from http://files.rcsb.org/download/5c7q.cif Fetching CCD PG0 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/0/PG0/PG0.cif 5c7q title: Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase [more info...] Chain information for 5c7q #13 --- Chain | Description | UniProt A B | NudF protein | Q6MIH8_BDEBA 1-182 Non-standard residues in 5c7q #13 --- GOL — glycerol (glycerin; propane-1,2,3-triol) PEG — di(hydroxyethyl)ether PG0 — 2-(2-methoxyethoxy)ethanol (peg 6000) PGE — triethylene glycol SO4 — sulfate ion 31 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 1 extra chains, 29 C-terminal residues, 38 N-terminal residues, 277 non-polymer residues more than 3.0 Angstroms away. Alignment of 5c7q chain B to query has RMSD 0.907 using 64 of 103 paired residues within cutoff distance 2.0 > open 1viu Summary of feedback from opening 1viu fetched from pdb --- note | Fetching compressed mmCIF 1viu from http://files.rcsb.org/download/1viu.cif 1viu title: Crystal structure of putative ADP ribose pyrophosphatase [more info...] Chain information for 1viu #14 --- Chain | Description | UniProt A B C D | ADP-ribose pyrophosphatase | YFFH_ECOLI 2-191 1viu mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly Deleted 3 extra chains, 27 C-terminal residues, 42 N-terminal residues, 123 non-polymer residues more than 3.0 Angstroms away. Alignment of 1viu chain A to query has RMSD 0.894 using 58 of 100 paired residues within cutoff distance 2.0 > open 6u9x Summary of feedback from opening 6u9x fetched from pdb --- note | Fetching compressed mmCIF 6u9x from http://files.rcsb.org/download/6u9x.cif 6u9x title: Structure of T. brucei MERS1-RNA complex [more info...] Chain information for 6u9x #15 --- Chain | Description | UniProt A D | Mitochondrial edited mRNA stability factor 1 | B6SBM0_9TRYP 37-395 H K | RNA (5'-R(*GP*AP*GP*AP*GP*GP*GP*GP*GP*UP*U)-3') | 6u9x mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| software_defined_assembly 4| software_defined_assembly Deleted 3 extra chains, 77 C-terminal residues, 105 N-terminal residues, 30 non-polymer residues more than 3.0 Angstroms away. Alignment of 6u9x chain D to query has RMSD 0.939 using 57 of 98 paired residues within cutoff distance 2.0 > open 6zse Summary of feedback from opening 6zse fetched from pdb --- warning | Expected gap or connection between 004 /A:7 and MHT /A:8 notes | Fetching compressed mmCIF 6zse from http://files.rcsb.org/download/6zse.cif Fetching CCD 004 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/004/004.cif Fetching CCD DBB from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/DBB/DBB.cif Fetching CCD DOL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/DOL/DOL.cif Fetching CCD MHT from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/MHT/MHT.cif Fetching CCD MHU from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/MHU/MHU.cif Fetching CCD MHV from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/V/MHV/MHV.cif Fetching CCD MHW from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/MHW/MHW.cif Fetching CCD P5P from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/P5P/P5P.cif Fetching CCD Y5P from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/Y5P/Y5P.cif 6zse title: Human mitochondrial ribosome in complex with mRNA, A/P-tRNA and P/E-tRNA [more info...] Chain information for 6zse #16 --- Chain | Description | UniProt 0 | 39S ribosomal protein L32, mitochondrial | RM32_HUMAN 1-188 1 | 39S ribosomal protein L33, mitochondrial | RM33_HUMAN 1-65 2 | 39S ribosomal protein L34, mitochondrial | RM34_HUMAN 1-92 3 | 39S ribosomal protein L35, mitochondrial | RM35_HUMAN 1-188 4 | 39S ribosomal protein L36, mitochondrial | RM36_HUMAN 1-103 5 | 39S ribosomal protein L37, mitochondrial | RM37_HUMAN 1-423 6 | 39S ribosomal protein L38, mitochondrial | RM38_HUMAN 1-380 7 | 39S ribosomal protein L39, mitochondrial | RM39_HUMAN 1-338 8 | 39S ribosomal protein L40, mitochondrial | RM40_HUMAN 1-206 9 | 39S ribosomal protein L41, mitochondrial | RM41_HUMAN 1-137 A | Quinupristin | A0 | 28S ribosomal protein S34, mitochondrial | RT34_HUMAN 1-218 A1 | 28S ribosomal protein S35, mitochondrial | RT35_HUMAN 1-323 A2 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 | CHCH1_HUMAN 1-118 A3 | Aurora kinase A-interacting protein | AKIP_HUMAN 1-199 A4 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial | PTCD3_HUMAN 1-689 AA | 12S mitochondrial rRNA | AB | 28S ribosomal protein S2, mitochondrial | RT02_HUMAN 1-296 AC | 28S ribosomal protein S24, mitochondrial | RT24_HUMAN 1-167 AD | 28S ribosomal protein S5, mitochondrial | RT05_HUMAN 1-430 AE | 28S ribosomal protein S6, mitochondrial | RT06_HUMAN 1-125 AF | 28S ribosomal protein S7, mitochondrial | RT07_HUMAN 1-242 AG | 28S ribosomal protein S9, mitochondrial | RT09_HUMAN 1-396 AH | 28S ribosomal protein S10, mitochondrial | RT10_HUMAN 1-201 AI | 28S ribosomal protein S11, mitochondrial | RT11_HUMAN 1-194 AJ | 28S ribosomal protein S12, mitochondrial | RT12_HUMAN 1-138 AK | 28S ribosomal protein S14, mitochondrial | RT14_HUMAN 1-128 AL | 28S ribosomal protein S15, mitochondrial | RT15_HUMAN 1-257 AM | 28S ribosomal protein S16, mitochondrial | RT16_HUMAN 1-137 AN | 28S ribosomal protein S17, mitochondrial | RT17_HUMAN 1-130 AO | 28S ribosomal protein S18b, mitochondrial | RT18B_HUMAN 1-258 AP | 28S ribosomal protein S18c, mitochondrial | RT18C_HUMAN 1-142 AQ | 28S ribosomal protein S21, mitochondrial | RT21_HUMAN 1-87 AR | 28S ribosomal protein S22, mitochondrial | RT22_HUMAN 1-360 AS | 28S ribosomal protein S23, mitochondrial | RT23_HUMAN 1-190 AT | 28S ribosomal protein S25, mitochondrial | RT25_HUMAN 1-173 AU | 28S ribosomal protein S26, mitochondrial | RT26_HUMAN 1-205 AV | 28S ribosomal protein S27, mitochondrial | RT27_HUMAN 1-414 AW | 28S ribosomal protein S28, mitochondrial | RT28_HUMAN 1-187 AX | 28S ribosomal protein S29, mitochondrial | RT29_HUMAN 1-398 AY | 28S ribosomal protein S31, mitochondrial | RT31_HUMAN 1-395 AZ | 28S ribosomal protein S33, mitochondrial | RT33_HUMAN 1-106 XA | 16S mitochondrial rRNA | XB | mitochondrial tRNAVal | XD | 39S ribosomal protein L2, mitochondrial | RM02_HUMAN 1-305 XE | 39S ribosomal protein L3, mitochondrial | RM03_HUMAN 1-348 XF | 39S ribosomal protein L4, mitochondrial | RM04_HUMAN 1-311 XH | 39S ribosomal protein L9, mitochondrial | RM09_HUMAN 1-267 XI | 39S ribosomal protein L10, mitochondrial | RM10_HUMAN 1-261 XJ | 39S ribosomal protein L11, mitochondrial | RM11_HUMAN 1-190 XK | 39S ribosomal protein L13, mitochondrial | RM13_HUMAN 1-178 XL | 39S ribosomal protein L14, mitochondrial | RM14_HUMAN 1-145 XM | 39S ribosomal protein L15, mitochondrial | RM15_HUMAN 1-296 XN | 39S ribosomal protein L16, mitochondrial | RM16_HUMAN 1-251 XO | 39S ribosomal protein L17, mitochondrial | RM17_HUMAN 1-175 XP | 39S ribosomal protein L18, mitochondrial | RM18_HUMAN 0-179 XQ | 39S ribosomal protein L19, mitochondrial | RM19_HUMAN 1-292 XR | 39S ribosomal protein L20, mitochondrial | RM20_HUMAN 1-149 XS | 39S ribosomal protein L21, mitochondrial | RM21_HUMAN 1-205 XT | 39S ribosomal protein L22, mitochondrial | RM22_HUMAN 7-212 XU | 39S ribosomal protein L23, mitochondrial | RM23_HUMAN 1-153 XV | 39S ribosomal protein L24, mitochondrial | RM24_HUMAN 1-216 XW | 39S ribosomal protein L27, mitochondrial | RM27_HUMAN 1-148 XX | 39S ribosomal protein L28, mitochondrial | RM28_HUMAN 1-256 XY | 39S ribosomal protein L47, mitochondrial | RM47_HUMAN 1-250 XZ | 39S ribosomal protein L30, mitochondrial | RM30_HUMAN 1-161 a | 39S ribosomal protein L42, mitochondrial | RM42_HUMAN 1-142 b | 39S ribosomal protein L43, mitochondrial | RM43_HUMAN 1-215 c | 39S ribosomal protein L44, mitochondrial | RM44_HUMAN 1-332 d | 39S ribosomal protein L45, mitochondrial | RM45_HUMAN 8-306 e | 39S ribosomal protein L46, mitochondrial | RM46_HUMAN 1-279 f | 39S ribosomal protein L48, mitochondrial | RM48_HUMAN 1-212 g | 39S ribosomal protein L49, mitochondrial | RM49_HUMAN 1-166 h | 39S ribosomal protein L50, mitochondrial | RM50_HUMAN 1-158 i | 39S ribosomal protein L51, mitochondrial | RM51_HUMAN 1-128 j | 39S ribosomal protein L52, mitochondrial | RM52_HUMAN 1-123 k | 39S ribosomal protein L53, mitochondrial | RM53_HUMAN 1-112 l | 39S ribosomal protein L54, mitochondrial | RM54_HUMAN 1-138 m | 39S ribosomal protein L55, mitochondrial | RM55_HUMAN 1-127 o | Ribosomal protein 63, mitochondrial | RT63_HUMAN 1-102 p | Peptidyl-tRNA hydrolase ICT1, mitochondrial | ICT1_HUMAN 1-206 q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 | G45IP_HUMAN 1-222 r | 39S ribosomal protein S18a, mitochondrial | RT18A_HUMAN 1-196 r1 | mRNA | r2 | A/P-tRNA | r3 | P/E-tRNA | s | 39S ribosomal protein S30, mitochondrial | RT30_HUMAN 1-439 t1 t2 t3 t4 t5 t6 | 39S ribosomal protein L12, mitochondrial | RM12_HUMAN -60-137 Non-standard residues in 6zse #16 --- 004 — (2S)-amino(phenyl)ethanoic acid (L-Phenylglycine) DBB — D-α-aminobutyric acid DOL — 5-(2-diethylamino- ethanesulfonyl)-21-hydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triaza- tricyclo[23.2.1.00,255]octacosa-1(27),12,17,19,25(28)-pentaene-2,8,14,23-tetraone (dalfopristin) GTP — guanosine-5'-triphosphate MG — magnesium ion MHT — (3S)-3-(methylsulfanyl)-1-azabicyclo[2.2.2]octane MHV — 4-oxo-L-pipecolic acid MHW — 3-hydroxypicolinic acid Y5P — 1-(5-O-phosphono-beta-D-ribofuranosyl)-1,4-dihydropyrimidine (pyrimidine riboside-5'-monophosphate) ZN — zinc ion 20 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Deleted 92 extra chains, 49 N-terminal residues, 204 non-polymer residues more than 3.0 Angstroms away. Alignment of 6zse chain e to query has RMSD 1.29 using 6 of 134 paired residues within cutoff distance 2.0 > close #16 > close #13#10-12,14-15 > show #!8 models > show #!9 models > close #8 > show #!6 models > close #6 > show #5 models > hide #5 models > show #2 models > similarstructures ligands > hide #2 models > show #!3 models > hide #!3 models > show #2 models > show #!7 models > hide #!7 models > show #!7 models > close #7 > show #5 models > hide #5 models > show #!4 models > hide #!4 models > show #!3 models > hide #!9 models > hide #!3 models > hide #2 models > hide #!1 models > show #!1 models > select add #1 5458 atoms, 5210 bonds, 18 pseudobonds, 1018 residues, 2 models selected > coulombic sel The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: ADPR-TK2284-NEB7-5_refine_061.pdb #1/L MET 1 ADPR-TK2284-NEB7-5_refine_061.pdb #1/L LYS 9 ADPR-TK2284-NEB7-5_refine_061.pdb #1/L ARG 12 ADPR-TK2284-NEB7-5_refine_061.pdb #1/L SER 18 ADPR-TK2284-NEB7-5_refine_061.pdb #1/L GLU 22 ADPR-TK2284-NEB7-5_refine_061.pdb #1/L LYS 24 ADPR-TK2284-NEB7-5_refine_061.pdb #1/L LYS 29 ADPR-TK2284-NEB7-5_refine_061.pdb #1/L GLU 33 ADPR-TK2284-NEB7-5_refine_061.pdb #1/L GLU 35 ADPR-TK2284-NEB7-5_refine_061.pdb #1/L HIS 37 ADPR-TK2284-NEB7-5_refine_061.pdb #1/L ARG 38 ADPR-TK2284-NEB7-5_refine_061.pdb #1/L LYS 58 ADPR-TK2284-NEB7-5_refine_061.pdb #1/L LYS 131 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M ASP 2 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M ARG 3 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M TYR 4 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M LEU 6 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M ARG 12 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M ASP 15 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M SER 18 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M ARG 20 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M ASP 21 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M GLU 22 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M GLU 28 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M GLU 33 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M GLU 35 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M LYS 131 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M LYS 137 ADPR-TK2284-NEB7-5_refine_061.pdb #1/M GLU 145 ADPR-TK2284-NEB7-5_refine_061.pdb #1/N LYS 24 ADPR-TK2284-NEB7-5_refine_061.pdb #1/N LYS 29 ADPR-TK2284-NEB7-5_refine_061.pdb #1/N GLU 33 ADPR-TK2284-NEB7-5_refine_061.pdb #1/N ARG 38 ADPR-TK2284-NEB7-5_refine_061.pdb #1/N GLU 91 ADPR-TK2284-NEB7-5_refine_061.pdb #1/O ARG 12 ADPR-TK2284-NEB7-5_refine_061.pdb #1/O GLU 127 ADPR-TK2284-NEB7-5_refine_061.pdb #1/O LYS 131 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for ADPR-TK2284-NEB7-5_refine_061.pdb_L SES surface #1.2: minimum, -27.09, mean -4.38, maximum 7.80 Coulombic values for ADPR-TK2284-NEB7-5_refine_061.pdb_M SES surface #1.3: minimum, -27.18, mean -2.21, maximum 8.76 Coulombic values for ADPR-TK2284-NEB7-5_refine_061.pdb_N SES surface #1.4: minimum, -20.63, mean -3.56, maximum 6.22 Coulombic values for ADPR-TK2284-NEB7-5_refine_061.pdb_O SES surface #1.5: minimum, -26.52, mean -2.91, maximum 8.80 To also show corresponding color key, enter the above coulombic command and add key true > hide sel surfaces > select clear Drag select of 3 atoms, 3 residues, 3 bonds > select clear > hide #!1 models > show #2 models > select :91 73 atoms, 61 bonds, 12 residues, 5 models selected > show sel & #2 atoms > hide #2 models > show #!1 models > select clear > close #1 > open /Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/ADPR-TK2284-NEB7-5_refine_068-coot-1.pdb Chain information for ADPR-TK2284-NEB7-5_refine_068-coot-1.pdb #1 --- Chain | Description L | No description available M | No description available N | No description available O | No description available 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure Drag select of 4 atoms, 38 residues, 3 bonds > select clear > show #2 models > close #1-2,5#3-4,9 > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Manuscript/TK2284 Structure Manuscript/New > Figure 4/Image of Assymetric Bending of the N-terminst.cxs"" > view name session-start opened ChimeraX session > open /Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/ADPR-TK2284-NEB7-5_refine_068-coot-1.pdb Chain information for ADPR-TK2284-NEB7-5_refine_068-coot-1.pdb #7 --- Chain | Description L | No description available M | No description available N | No description available O | No description available 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/ADPR-TK2284-NEB7-5_refine_068-coot-1 copy.pdb"" Chain information for ADPR-TK2284-NEB7-5_refine_068-coot-1 copy.pdb #8 --- Chain | Description L | No description available M | No description available N | No description available O | No description available 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure Cell requested for row 5 is out of bounds for table with 9 rows! Resizing table model. > hide #!6 models > hide #7 models > hide #!1 models > select #8/L:158 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 63 atoms, 63 bonds, 8 residues, 1 model selected > select up 1236 atoms, 1260 bonds, 166 residues, 1 model selected > select up 5464 atoms, 5210 bonds, 1026 residues, 1 model selected > select down 1236 atoms, 1260 bonds, 166 residues, 1 model selected > delete sel > select clear > select #8/M:86 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 107 atoms, 106 bonds, 13 residues, 1 model selected > select up 1244 atoms, 1268 bonds, 168 residues, 1 model selected > delete sel Drag select of 51 atoms, 28 bonds > delete sel > show #7 models > hide #8 models > select #7/N:157 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 63 atoms, 63 bonds, 8 residues, 1 model selected > select up 1279 atoms, 1304 bonds, 167 residues, 1 model selected > delete sel > select clear > select #7/O:83 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 107 atoms, 106 bonds, 13 residues, 1 model selected > select up 1295 atoms, 1320 bonds, 167 residues, 1 model selected > delete sel > select clear Drag select of 56 atoms, 2 residues, 34 bonds > select clear Drag select of 8 atoms, 3 residues, 6 bonds > select clear Drag select of 52 atoms, 28 bonds > delete sel > select clear > show #8 models > show #!1 models > view #1 clip false > mmaker #7 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Ca_8oxoATP_refine_033-FINAL.pdb, chain A (#1) with ADPR- TK2284-NEB7-5_refine_068-coot-1.pdb, chain M (#7), sequence alignment score = 845 RMSD between 122 pruned atom pairs is 0.530 angstroms; (across all 166 pairs: 2.660) > mmaker #8 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Ca_8oxoATP_refine_033-FINAL.pdb, chain A (#1) with ADPR- TK2284-NEB7-5_refine_068-coot-1 copy.pdb, chain O (#8), sequence alignment score = 842.6 RMSD between 156 pruned atom pairs is 0.544 angstroms; (across all 166 pairs: 1.003) > dssp > hide #7 models > show #7 models > hide #8 models Drag select of 7 residues, 1 atoms, 2 bonds > select clear > hide #!1 models > show #8 models Drag select of 12 residues, 3 atoms, 2 bonds > select clear Drag select of 2 residues > select clear Drag select of 2 atoms, 35 residues, 1 bonds > select #7/M:81 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > show #!1 models > hide #7 models > hide #8 models > show #8 models > hide #!1 models > show #!1 models > select add #1 2707 atoms, 2653 bonds, 441 residues, 1 model selected > select add #8 5640 atoms, 5306 bonds, 1108 residues, 4 models selected > show sel atoms > select clear Drag select of 7 atoms, 4 residues, 6 bonds > select clear > hide #!1 models > show #7 models > show #7-8 atoms > undo > show #7 models > hide #!1 models > select #8:1-39 673 atoms, 636 bonds, 128 residues, 1 model selected > ui tool show Axes/Planes/Centroids > define centroid sel Centroid 'centroid' placed at [ 11.17406686 -11.45223477 41.59986924] > select #7:1-39 581 atoms, 543 bonds, 126 residues, 1 model selected > define centroid sel Centroid 'centroid' placed at [13.33047676 59.13523064 15.96178657] centroid #7.1 to centroid #8.1: distance: 2.913Å > distance > #!7/A:1#!7/A:5#!7/B:11#!7/B:12#!7/B:13#!7/B:14#!7/C:1#!7/C:2#!7/C:3#!7/C:4#!7/C:5#!7/C:17#!7/C:18#!7/C:19#!7/C:20#!7/C:22#!7/C:23#!7/C:24#!7/C:25#!7/C:26#!7/C:27#!7/C:28#!7/C:29#!7/C:30#!7/C:31#!7/C:32#!7/C:33#!7/D:2#!7/D:3#!7/D:4#!7/L:1#!7/L:2#!7/L:3#!7/L:4#!7/L:5#!7/L:6#!7/L:7#!7/L:8#!7/L:9#!7/L:10#!7/L:11#!7/L:12#!7/L:13#!7/L:14#!7/L:15#!7/L:16#!7/L:17#!7/L:18#!7/L:19#!7/L:20#!7/L:21#!7/L:22#!7/L:23#!7/L:24#!7/L:25#!7/L:26#!7/L:27#!7/L:28#!7/L:29#!7/L:30#!7/L:31#!7/L:32#!7/L:33#!7/L:34#!7/L:35#!7/L:36#!7/L:37#!7/L:38#!7/L:39#!7/M:1#!7/M:2#!7/M:3#!7/M:4#!7/M:5#!7/M:6#!7/M:7#!7/M:8#!7/M:9#!7/M:10#!7/M:11#!7/M:12#!7/M:13#!7/M:14#!7/M:15#!7/M:16#!7/M:17#!7/M:18#!7/M:19#!7/M:20#!7/M:21#!7/M:22#!7/M:23#!7/M:24#!7/M:25#!7/M:26#!7/M:27#!7/M:28#!7/M:29#!7/M:30#!7/M:31#!7/M:32#!7/M:33#!7/M:34#!7/M:35#!7/M:36#!7/M:37#!7/M:38#!7/M:39#!7/S:16#!7/S:20#!7/S:21#!7/S:23#!7/S:24#!7/S:25#!7/S:26#!7/S:27#!7/S:28#!7/S:29#!7/S:30#!7/S:31#!7/S:33#!7/S:34#!7/S:35#!7/S:36#!7/S:37#!7/S:39 > #7.1#8.1 Distance between centroid #7.1 and 581 atoms: min 1.054Å (ADPR- TK2284-NEB7-5_refine_068-coot-1.pdb #!7/L LEU 6 N), average: 13.921Å, max 72.681Å (ADPR-TK2284-NEB7-5_refine_068-coot-1.pdb #!7/S HOH 34 O) Distance between centroid #8.1 and 581 atoms: min 1.534Å (ADPR- TK2284-NEB7-5_refine_068-coot-1.pdb #!7/L LEU 6 C), average: 14.353Å, max 71.864Å (ADPR-TK2284-NEB7-5_refine_068-coot-1.pdb #!7/S HOH 34 O) > select clear > hide #!7 models > show #!7 models > select clear > select #7.1 1 atom, 1 residue, 1 model selected > select add #8.1 2 atoms, 2 residues, 2 models selected > distance #7.1 #8.1 Distance between centroid #7.1 and centroid #8.1: 2.913Å > close #7.1#8.1 > select #7:1-37 552 atoms, 514 bonds, 121 residues, 1 model selected > define centroid sel Centroid 'centroid' placed at [13.3955942 59.54851268 15.66290217] > select #7:1-36 542 atoms, 504 bonds, 119 residues, 2 models selected > define centroid sel Centroid 'centroid' placed at [23.76848081 36.10778151 12.79497378] centroid #7.1 to centroid #10: distance: 0.170Å > close #10#7.1 > define centroid sel Centroid 'centroid' placed at [13.36444547 59.70951017 15.61769501] > select #8:1-36 622 atoms, 585 bonds, 119 residues, 1 model selected > define centroid sel Centroid 'centroid' placed at [ 11.25092926 -11.90938424 41.93952572] > select clear > select #8.1 1 atom, 1 residue, 1 model selected > select add #7.1 2 atoms, 2 residues, 2 models selected > distance #8.1 #7.1 Distance between centroid #8.1 and centroid #7.1: 3.031Å > hide #!7 models > show #!1 models > hide #!8 models > hide #9.1 models > hide #!9 models > show #!8 models > show #!7 models > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Manuscript/TK2284 Structure Manuscript/New > Figure 4/Overall View 1.cxs"" > view name session-start opened ChimeraX session > open /Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Last-Refinement.pdb Chain information for Last-Refinement.pdb #6 --- Chain | Description L | No description available M | No description available N | No description available O | No description available 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > mmaker #6 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Ca_8oxoATP_refine_033-FINAL.pdb, chain A (#1) with Last- Refinement.pdb, chain M (#6), sequence alignment score = 845 RMSD between 123 pruned atom pairs is 0.560 angstroms; (across all 166 pairs: 2.626) > hide #6 models > hide #!5.1 models > hide #!5 models > show #6 models > hide #!1 models > cartoon style thickness 1.2 > cartoon style width 2.5 > show #!1 models > show #!5 models > hide #!5 models > show #!5.1 models Drag select of 47 residues > select clear > open /Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/Refine_82/ADPR-TK2284-NEB7-5_refine_082.pdb Chain information for ADPR-TK2284-NEB7-5_refine_082.pdb #7 --- Chain | Description L | No description available M | No description available N | No description available O | No description available 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > mmaker #7 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Ca_8oxoATP_refine_033-FINAL.pdb, chain A (#1) with ADPR- TK2284-NEB7-5_refine_082.pdb, chain M (#7), sequence alignment score = 845 RMSD between 123 pruned atom pairs is 0.560 angstroms; (across all 166 pairs: 2.626) > cartoon style thickness 1.2 > cartoon style width 2.5 > hide #!5 models > show #!5 models > hide #6 models > hide #!5.1 models > show #!5.1 models Drag select of 10 residues > select clear > dssp > close #7 > close #6 > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Manuscript/TK2284 Structure > Manuscript/ADPR_TK2284_Refine_84/ADPR-TK2284-NEB7-5_refine_084.pdb"" Chain information for ADPR-TK2284-NEB7-5_refine_084.pdb #6 --- Chain | Description L | No description available M | No description available N | No description available O | No description available 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Manuscript/TK2284 Structure Manuscript/New > Figure 4/Image of Assymetric Bending of the N-terminst.cxs"" > view name session-start opened ChimeraX session > hide #!6 models > open ""/Users/mbanco/Library/CloudStorage/OneDrive- > NewEnglandBiolabs/Documents/Manuscript/TK2284 Structure > Manuscript/ADPR_TK2284_Refine_84/ADPR-TK2284-NEB7-5_refine_084.pdb"" Chain information for ADPR-TK2284-NEB7-5_refine_084.pdb #7 --- Chain | Description L | No description available M | No description available N | No description available O | No description available 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure > mmaker #7 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Ca_8oxoATP_refine_033-FINAL.pdb, chain A (#1) with ADPR- TK2284-NEB7-5_refine_084.pdb, chain M (#7), sequence alignment score = 845 RMSD between 123 pruned atom pairs is 0.561 angstroms; (across all 166 pairs: 2.624) > select #7/O:161 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 63 atoms, 63 bonds, 8 residues, 1 model selected > select up 1295 atoms, 1320 bonds, 167 residues, 1 model selected > hide sel cartoons > select #7/N:98 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 55 atoms, 55 bonds, 7 residues, 1 model selected > select up 1274 atoms, 1299 bonds, 166 residues, 1 model selected > select up 5463 atoms, 5210 bonds, 1025 residues, 1 model selected > select clear > select #7/M:168 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 48 atoms, 48 bonds, 6 residues, 1 model selected > select up 1249 atoms, 1273 bonds, 169 residues, 1 model selected > select clear > select #7/N:97 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 55 atoms, 55 bonds, 7 residues, 1 model selected > select up 1274 atoms, 1299 bonds, 166 residues, 1 model selected > hide sel cartoons > select clear > hide #7#!1 atoms > cartoon style thickness 1.2 > cartoon style width 2.5 > color #1 #009051ff > color #1 #008f00ff > color #1 #4f8f00ff > color #1 #929000ff > color #1 #fffb00ff > color #1 #00f900ff > color #1 #d783ffff > color #1 #ff9300ff > color #1 #ff2600ff > color #1 #ff9300ff > color #1 #945200ff > color #1 #929000ff > color #1 #fffb00ff > color #1 #945200ff > color #1 #0096ffff > color #1 #9437ffff > color #1 silver > color #1 #d6d6d6ff > color #1 silver > color #1 darkgrey > color #1 #00fa92ff > color #1 #00f900ff > color #1 #8efa00ff > color #1 #fffb00ff > color #1 #0433ffff > color #1 #9437ffff > color #1 #7a81ffff > color #1 #d783ffff > color #1 #73fdffff > color #1 #73fcd6ff > color #1 #d4fb79ff > color #1 #fffc79ff > color #1 #fffb00ff > color #1 #fffc79ff > color #1 #ffd479ff > color #1 #7a81ffff > color #1 #0433ffff > color #1 #011993ff > color #1 #005493ff > color #1 #009193ff > color #1 #ff40ffff > color #1 #531b93ff > color #1 #005493ff > color #1 #009193ff > color #1 #005493ff > color #7 silver > color #7 #929292ff > color #7 darkgrey > ui tool show ""Side View"" > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > select add #1 2707 atoms, 2653 bonds, 441 residues, 1 model selected > ui tool show ""Color Actions"" > color sel gold > color sel saddle brown > color sel brown > color sel wheat > color sel azure > color sel wheat > color sel white smoke > color sel pale turquoise > color sel light sky blue > color sel sky blue > color sel light sky blue > color sel sky blue > color sel light sky blue > color sel light blue > color sel sky blue > color sel light sky blue > color sel sky blue > select clear > select add #7 5463 atoms, 5210 bonds, 1025 residues, 1 model selected > color sel light coral > color sel tan > color sel rosy brown > color sel dark sea green > color sel rebecca purple > color sel hot pink > color sel orchid > color sel pale violet red > color sel midnight blue > color sel dark slate gray > color sel dark olive green > color sel sea green > color sel green > color sel forest green > select clear > select add #7 5463 atoms, 5210 bonds, 1025 residues, 1 model selected > color sel dark blue > color sel dark green > color sel tan > color sel burly wood > color sel tan > color sel rosy brown > color sel tan > color sel plum > color sel light cyan > color sel plum > color sel cornflower blue > color sel medium blue > color sel magenta > color sel dim gray > color sel purple > color sel hot pink > color sel magenta > color sel light blue > color sel silver > color sel powder blue > color sel light gray > color sel thistle > color sel tan > color sel burly wood > color sel tan > color sel rosy brown > color sel tan > select add #1 8170 atoms, 7863 bonds, 1466 residues, 2 models selected > select subtract #7 2707 atoms, 2653 bonds, 441 residues, 3 models selected > color sel rosy brown > color sel dark gray > color sel rosy brown > color sel light coral > color sel rosy brown > color sel dark sea green > color sel medium sea green > color sel sea green > color sel cyan > color sel deep sky blue > color sel cadet blue > color sel steel blue > color sel cadet blue > color sel steel blue > color sel teal > color sel steel blue > select clear > select add #7 5463 atoms, 5210 bonds, 1025 residues, 1 model selected > color sel deep sky blue > color sel steel blue > color sel medium aquamarine > color sel light sea green > color sel turquoise > color sel dodger blue > color sel tan > color sel rosy brown > color sel tan > color sel burly wood > color sel tan > color sel burly wood > color sel wheat > color sel pale goldenrod > color sel burly wood > select clear > show #!5 models > show #!6 models > hide #!6 models > hide #!5 models > show #!6 models > hide #!6 models > dssp Drag select of 16 residues > select clear Drag select of 22 residues > select clear > show #7#!1 atoms Drag select of 4 atoms, 5 residues, 3 bonds > select clear > undo Drag select of 11 atoms, 11 residues, 10 bonds > select clear > undo > select clear > undo > select #1:40-50,70-127,150-300 1418 atoms, 1395 bonds, 219 residues, 1 model selected > transparency #1:40-50,70-127,150-300 50 cartoons > transparency #7:40-50,70-127,150-300 50 cartoons > save /Users/mbanco/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/test.tif width 3041 height 2001 supersample 4 transparentBackground > true > show #!6 models > hide #!6 models > transparency #7:40-50,70-127,150-300 75 cartoons > select add #7 5463 atoms, 5210 bonds, 1025 residues, 1 model selected > ui tool show ""Color Actions"" > color sel khaki > color sel pale goldenrod > color sel moccasin > color sel navajo white > color sel peach puff > color sel pink > color sel light pink > color sel antique white > color sel linen > color sel ivory > color sel snow > color sel violet > color sel light cyan > color sel plum > color sel thistle > color sel alice blue > color sel pale violet red > color sel dark slate gray > color sel bisque > color sel peach puff > color sel pink > color sel old lace > color sel light goldenrod yellow > color sel antique white > color sel ghost white > color sel beige > color sel wheat > color sel khaki > color sel pale goldenrod > select clear > select ::name=""OXO"" 64 atoms, 68 bonds, 2 residues, 2 models selected > show sel & #!1 atoms > color (#!1 & sel) yellow > color (#!1 & sel) byhetero > select clear > select add #7 5463 atoms, 5210 bonds, 1025 residues, 1 model selected > color sel plum > color sel old lace > color sel thistle > color sel peach puff > select clear > show #!6 models > hide #!6 models > select :rib 56 atoms, 56 bonds, 4 residues, 1 model selected > show sel atoms > style sel ball Changed 56 atom styles > color sel byhetero > select clear > transparency 0 cartoons > transparency #7:40-50,105-117,70-127,150-300 75 cartoons > transparency #1:40-50,105-117,70-127,150-300 75 cartoons > transparency #1:40-50,105-117,70-127,150-300 0 cartoons > transparency #7:40-50,105-117,70-127,150-300 75 cartoons > transparency #1:40-50,105-117,70-127,150-300 75 cartoons > transparency #1:40-50,70-105,117-127,150-300 75 cartoons > transparency #1:40-50,105-117,70-127,150-300 0 cartoons > transparency 0 cartoons > transparency #1:40-50,70-105,117-127,150-300 75 cartoons > transparency #7:40-50,70-105,117-127,150-300 75 cartoons > select clear > save /Users/mbanco/Documents/Science/TK2284/Structures/TK2284-ADPR- > NEB7-5/test.tif width 3041 height 2001 supersample 4 > show #!6 models > hide #!6 models > transparency #7:40-50,70-105,117-127,150-300 85 cartoons > transparency #1:40-50,70-105,117-127,150-300 85 cartoons > transparency #1:40-50,70-108,117-127,150-300 85 cartoons > transparency #7:40-50,70-108,117-127,150-300 85 cartoons > select clear Drag select of 14 atoms, 14 bonds > hide sel atoms Drag select of 13 atoms, 13 bonds > select clear Drag select of 14 atoms, 14 bonds > hide sel atoms Drag select of 4 residues > select clear > save ""/Users/mbanco/Documents/Manuscript/TK2284 Structure Manuscript/New > Figure 4/test.tif"" width 3041 height 2001 supersample 4 > color #7 #7a81ffff > color #7 #011993ff > color #7 #00fa92ff > color #7 #945200ff > undo > show #!6 models > transparency 75 surfaces > hide #!6 models > select add #7 5463 atoms, 5210 bonds, 1025 residues, 1 model selected > ui tool show ""Color Actions"" > color sel rosy brown > color sel honeydew > color sel beige > color sel wheat > color sel linen > color sel antique white > color sel light goldenrod yellow > color sel old lace > color sel pale goldenrod > color sel khaki > color sel burly wood > color sel tan > color sel rosy brown > select #7/L:65 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #7 5463 atoms, 5210 bonds, 1025 residues, 1 model selected > select subtract #7 Nothing selected > select add #7 5463 atoms, 5210 bonds, 1025 residues, 1 model selected > color sel bisque > color sel moccasin > color sel navajo white > color sel cornsilk > color sel seashell > color sel blanched almond > color sel khaki > color sel wheat > color sel alice blue > color sel khaki > select clear > select add #7 5463 atoms, 5210 bonds, 1025 residues, 1 model selected > select clear > select add #1 2707 atoms, 2653 bonds, 441 residues, 1 model selected > color sel cadet blue > color sel teal > color sel medium aquamarine > color sel dark cyan > color sel cornflower blue > color sel light sea green > color sel dodger blue > color sel deep sky blue > color sel teal > color sel medium aquamarine > color sel dark cyan > select clear > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10rc202505150242 (2025-05-15) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,9 Model Number: MPHE3LL/A Chip: Apple M2 Pro Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 13822.1.2 OS Loader Version: 13822.1.2 Software: System Software Overview: System Version: macOS 26.0.1 (25A362) Kernel Version: Darwin 25.0.0 Time since boot: 7 days, 21 hours, 21 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal HP V27i: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported LG HDR 4K: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.3.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.3.3 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.3 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.6 ChimeraX-AtomicLibrary: 14.1.18 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.2.6 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10rc202505150242 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.1 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.8.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.13.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 narwhals: 2.5.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 2.3.3 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 plotly: 6.3.0 pluggy: 1.5.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pyKVFinder: 0.8.2 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.3.5 pytest-cov: 6.1.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 26.4.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tomlkit: 0.13.3 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.13.2 tzdata: 2025.2 urllib3: 2.4.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect new normal Unassigned