90 EDO 1PE
337 MG EDO CA

Maybe those but probably nothing to be predicted.

Domenico
The above contacts are probably not very reliable, because of the nature of the interacting ligands themselves. However, template 3ckcA0 has been solved in complex with different sugars separately - pdb codes: 3ck7, 3ck8, 3ck9 and 3ckb. I would suggest using them to infer which residues are involved in binding. Manual inspection of these complexes reveals that the following amino acids are mainly responsible for binding:
Asp73, Arg81, Trp96, Trp98, Asn101, Tyr296, Trp320, Cys322
Genthreader alignment is not very useful, as it maps all but one of these template residues to gaps. I have generated an alignment between the the target sequence, the template 3ck7A and other similar structures through SAS and obtained this prediction: Asp32, Ser40, Ala55, Lys57, Ile60, Tyr262, Tyr283, Ala 285.
I have to say that I'm not totally satisfied with it, as these amino acids do not come together in the Bioserf 3D model - because the templates 3ckcA0 was not used for modelling I guess. Yet, this is probably the best we can do based on sequence data:

PFRMAT FN
TARGET T0532
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: 32, 40, 55, 57, 60, 262, 283, 285
END

NO SUBMISSION FOR THIS TARGET

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« This page (revision-1) was last changed on 01-Jun-2010 17:57 by UnknownAuthor