Delta-1 loop interactions with the underlying surface of the hepatitis C virus RNA-dependent RNA polymerase (Protein Data Bank entry 1quv). To make this image, two copies of the structure were loaded and residues 15-41 (delta-1 loop) were deleted from one copy. The surface of the truncated model is shown. The second model is represented as a ribbon in blue. Van der Waals clashes/contacts between the loop and the surface ≥ 0.01 Å were found. The interacting residues of the loop are shown in stick form and colored according to atom. Interacting atoms of the underlying surface are colored red. The "publication 1" preset was used.
For an alternative approach that uses just one copy of the structure, see the Chimera command script 1quv.com.
Gallery entry courtesy of Ian Yarbrough, Department of Biochemistry and Biophysics, Texas A&M University. Similar images appear in the following:
Chinnaswamy S, Yarbrough I, Palaninathan S, Ranjith-Kumar CT, Vijayaraghavan V, Demeler B, Lemon SM, Sacchettini JC, Kao CC. A locking mechanism regulates RNA synthesis and host protein interaction by the hepatitis C virus polymerase. J Biol Chem 283(29):20535-20546 (2008).See also the Opened Interface image tutorial.
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