User:Eric Martz/AlphaFold3 case studies

From Proteopedia

Revision as of 21:43, 12 November 2024

In the following case studies of predictions by AlphaFold3, done in November 2024, superpositions and RMSD values were obtained from FATCAT. Animations were captured from FATCAT.

AlphaFold3 Example 8AW3

Q38107 (tRNA A34 deaminase) is the longest chain in the example 8aw3 provided by the AlphaFold3 Server. In 8aw3, its chain name is "3". 8aw3 is a cryo-EM structure with resolution 3.6 Å. 8aw3 indicates that the experimental material included full-length chain 3 of 369 residues, but 28 end-residues lack coordinates, so the coordinates run from UniProt 4-344, length 341. Within this range, there are two loops lacking coordinates of lengths 49 and 13, leaving 279 amino acids with coordinates. Neither missing loop is predicted to be disordered at UniProt, although the disorder estimate is high for both.

Q38107: AlphaFold3 vs Empirical Structure

The overall 4-chain prediction (for the complex in 8aw3) has pTM of 0.75, at the low end of the range 0.7-0.9 deemed "confident" by the server. Both of the missing loops have "no-confidence" (red) coordinates. The longer one is modeled as a large circle protruding from the surface of the protein, typical for loops with intrinsic disorder. The average pLDDT for chain 3 is 68 (weak confidence), but with the large disordered loop removed, this increases to 74.

The AlphaFold3 prediction superposes (FATCAT rigid) with 312 alpha carbons of chain 3 of 8aw3 with RMSD 2.2 Å.