AlphaFold2 examples from CASP 14: Difference between revisions
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===T1037 contains several known fold fragments=== | ===T1037 contains several known fold fragments=== | ||
(Dali | The X-ray structure of T1037 (404 residues from 6vr4) was submitted to Dali<ref name="dali2020" /> in March, 2021. Among the ~1,000 hits with Z ≥ 2.0, there were 152 with lengths ≥ 400 residues, and 224 with lengths ≥ 300, long enough that a superposition with the majority of T1037 would not be precluded. Among all hits, the largest number of aligned residues was 140/404 (35%) with RMSD 11.7 Å. The second largest was 127/404 (31%), RMSD 7.7 Å. Thus, no single structure in the PDB superposed with more than 35% of T1037. | ||
However, several of the Dali hits superposed with non-overlapping core fragments of [[6vr4]]: | |||
*[[2j7n]] chain A, RNA-dependent RNA polymerase | |||
**length 934, aligned residues '''115, RMSD 4.3 Å''', structural alignment 9 %id. | |||
*[[4ncj]] chain A, DNA double-strand break repair RAD50 ATPase | |||
**length 311, aligned residues '''109, RMSD 4.7 Å''', structural alignment 11 %id. | |||
*[[5vfk]] chain A, Uncharacterized protein | |||
**length 146, aligned residues '''61, RMSD 7.8 Å''', structural alignment 11 %id. | |||
The [https://fatcat.godziklab.org/ FATCAT Server] reported that in order to superpose 150 residues (37% of 404) of T1037 with the closest structure in the PDB, 3 twists at hinges were required, after which an RMSD of 3.1 Å was achieved. For a 200-residue superposition (50% of 404), the best results after 3 twists had an RMSD of 5.4 Å. | The [https://fatcat.godziklab.org/ FATCAT Server] reported that in order to superpose 150 residues (37% of 404) of T1037 with the closest structure in the PDB, 3 twists at hinges were required, after which an RMSD of 3.1 Å was achieved. For a 200-residue superposition (50% of 404), the best results after 3 twists had an RMSD of 5.4 Å. | ||
