AlphaFold Fetch

AlphaFold is an artificial intelligence method for predicting protein structures. With the AlphaFold tool or command, ChimeraX can search for and load predicted structures from the freely available AlphaFold Database, automatically coloring them by confidence value:

• 100 to 90 – high accuracy
• 90 to 70 – backbone accuracy
• 70 to 50 – low confidence, caution
• 50 to 0 – should not be interpreted, may be disordered

The figure shows the predicted structure of UniProt entry TOM40_HUMAN, a channel protein needed to import other proteins into mitochondria. See the command file tom40.cxc for fetching data and other setup (background color, etc.).

Opening a sequence from UniProt also opens a dialog in which its annotations or “features” can be clicked to highlight those regions in both the sequence and the associated 3D structure. The low-confidence part of this structure (orange and red) maps to compositionally biased and likely disordered regions near the N-terminus of the sequence.

Cyclodextrin Pore

The outer-membrane protein CymA admits bulky molecules into the periplasmic space of Klebsiella oxytoca. Here, CymA (PDB 4d5d chain A) is depicted in a style reminiscent of a diagnostic X-ray, with transparent molecular surface and β-strand “ribs” in white. The protein has ingested α-cyclodextrin (top) and β-cyclodextrin (bottom), bound at the entry site and near the exit, respectively. Cyclodextrin carbon atoms are shown in blue-gray and oxygen atoms in brick red. For image setup, see the command file xray.cxc.

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