Re: [ccp4bb] Ligand binding in multiple conformation

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Ligand binding in multiple conformation
From: Chandra Verma chandra {- at -} BII {- dot -} A-STAR {- dot -} EDU {- dot -} SG
Date: 2009-01-12

Next message:
Subject: Re: Ligand binding in multiple conformation
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2009-01-12

Subject: Re: Ligand binding in multiple conformation
From: Aaron Oakley Aaron {- dot -} Oakley {- at -} CSIRO {- dot -} AU
Date: 2009-01-12

>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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Ligand binding in multiple conformation
From: Chandra Verma chandra {- at -} BII {- dot -} A-STAR {- dot -} EDU {- dot -} SG
Date: 2009-01-12

Next message:
Subject: Re: Ligand binding in multiple conformation
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2009-01-12