[phenixbb] Ligand occupancy and conformational change

Xavier Brazzolotto xavier.brazzolotto at chemdef.fr
Tue Jul 24 08:01:06 PDT 2018

Thanks George

The residues of the loops are already assigned with ARESNAME and BRESNAME and it is ok to refine both loops

What I would like to do is then to add the ligand. But in the apo state it clashes with one residue of the loop.
So I thought fixing the occupancy to 0 (zero), for one ALT of the ligand (with apo loop) and having a second ALT with an occupancy <1 (bound loop) to try to prevent atom clashing.
Is it the right strategy ? And how to do it ?

Moreover, it seems to get more complicated as the bound ligand can also exist with at least 2 different alternatives (different orientation of a central indole ring).

> Le 24 juil. 2018 à 09:49, G_Kontopidis <gkontopidis at vet.uth.gr> a écrit :
> Hi Havier,
> You got the formula right 
> alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X
> You may have also some water include in the model correspond to alternate loop A" occupancy = X 
> I have done it many times using RefMac and SHELX I am sure it is working in Phenix as well .
> you do not need something specific in a parameter file for the protein atom.
> The PDB file look like the following.
> ATOM    258  CA AGLN A  35       2.979  -4.265  69.678  0.40 46.35           C
> ANISOU  258  CA AGLN A  35     4942   7133   5533      0    946   -219       C
> ATOM    259  CA BGLN A  35       3.127  -4.246  69.643  0.60 47.74           C
> ANISOU  259  CA BGLN A  35     5152   7285   5702      0    930   -219       C
> The alternative atom specified with letter A and B before the amino acid three letters.
> Regards,
> George
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Xavier Brazzolotto
> Sent: Tuesday, July 24, 2018 9:50 AM
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] Ligand occupancy and conformational change
> I am struggling with a ligand bound structure.
> The ligand seems to induce a small conformational change of one loop. However, despite my efforts I did not get any data with a full occupancy for this ligand yet.
> As a result, I have to deal with a loop in apo state (where ligand occupancy = 0) and a loop with a bound ligand (where ligand occupancy <1) and where the ligand is clashing with the modelled loop in the apo state.
> Hope I did myself clear.
> How to deal with this situation ? I am sure that phenix.refine can do it but how ?
> What I would like to try is something like that "alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X
> Maybe something specific in a parameter file ?
> Thank you for your help
> Xavier

Xavier Brazzolotto, PhD
xavier.brazzolotto at chemdef.fr

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