AlphaFold2 examples from CASP 14: Difference between revisions

← Older edit Newer edit →

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

@@ Line 94: / Line 94: @@
 **length 146, aligned residues '''61, RMSD 7.8 Å''', Z=3.3, structural alignment 11 %id.
-Liisa Holm<ref name="dali2020" /><ref name="holmquote">Quoted with permission from Liisa Holm, March, 2021.</ref> stated: "T1037 has a homologous template in the PDB. The parent structure of T1037, phage RNA polymerase (6vr4, 2166 amino acids), is homologous to the RNAi polymerase from Neurospora crassa (2j7nA, 934 amino acids)<ref name="6vr4" />. Dali aligns them over 564 residues with an RMSD of 4.8 A. 115 residues of the common core are in the T1037 substructure. Several long insertions in T1037/6vr4 relative to 2j7n (chain A) form subdomains, which point outwards from the common core. Similar massive adaptation of the common core is seen, for example, in the glucosyltransferase 1 family<ref>PMID: 7729407</ref>."
+Liisa Holm<ref name="dali2020" /><ref name="holmquote">Quoted with permission from Liisa Holm, March, 2021.</ref> stated: "T1037 has a homologous template in the PDB. The parent structure of T1037, phage RNA polymerase (6vr4, 2166 amino acids), is homologous to the RNAi polymerase from Neurospora crassa (2j7n chain A, 934 amino acids)<ref name="6vr4" />. Dali aligns them over 564 residues with an RMSD of 4.8 A. 115 residues of the common core are in the T1037 substructure. Several long insertions in T1037/6vr4 relative to 2j7n (chain A) form subdomains, which point outwards from the common core. Similar massive adaptation of the common core is seen, for example, in the glucosyltransferase 1 family<ref>PMID: 7729407</ref>."
 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.