An extension of this topic: does anyone know of examples where for
complexes between the two proteins A and B, protein A has two different
conformations at its interface?
thanks
chandra
-----Original Message-----
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Aaron Oakley
Sent: Tuesday, January 13, 2009 1:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Ligand binding in multiple conformation
I had a question about flexibility in ligand binding in an enzyme
active site.
Is it possible for a substrate/product analogue to bind in more than
one conformation in the active site.
Yes. It is even possible for portions of a ligand to be disordered and
not discernable in electron density.
Since the ligand/enzyme interactions are very specific I am a little
confused about this.
Also which program would you use if you have to refine with alternate
ligand conformation.
REFMAC will do this just fine. Just make sure you have the "A", "B"
conformers set in the PDB file.
EG:
ATOM 72 CA APRO A 7 -2.619 28.983 -0.796 0.62 6.48
C
ATOM 73 CA BPRO A 7 -2.226 29.044 -0.847 0.38 5.76
C
