Domenico:
We only have one confident template - 2vt3B0 - in complex with ATP. On the other hand the same protein has been solved in complex with NAD - PDB code 2vt2 - which looks more reasonable from a biological standpoint. Based on Genthreader's alignment, residues Tyr7, Gly8, Ala9, Gly10, Ser11, Asp33, Asp34, Lys38, Pro51, Ala69, Val70, Pro71, Gln75 and Ile81 are likely to form the binding site. Most of them are identically conserved and occur in the consensus from Dan's scripts. I think we should filter the above list using the conservation score from David's tool. Using a cut-off equal to 7, would give a very restrictive prediction - only Gly8, Asp33, Asp34 and Pro71 - so I'd suggest to include also those candidate positions with a conservation score equal to 6.

PFRMAT FN
TARGET T0622
AUTHOR 7656-5034-1890
REMARK Sequence consensus of contacts between homologous structures and ligands
METHOD pGenTHREADER and PDBSum and CSA data mining.
MODEL 1
Binding site: 8, 9, 10, 33, 34, 71
END

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« This page (revision-1) was last changed on 27-Jul-2010 12:42 by UnknownAuthor