[phenixbb] racemic ligand refinement

[Tanner, John J.]

Nic,

We encountered this situation – see PDB ID 7MYB. We assigned the two stereoisomers to have unique residue names, unique residue numbers, and different alternate location identifiers (the A and B before the residue name below). They can have the same chain ID. The A and B alternative location IDs prevent the molecules from clashing with each other. Here is how we set it up in our case:


HETATM18364  C02AUJM B1301      -4.302  21.083 108.824  0.50 33.60           C

HETATM18365  C04AUJM B1301      -5.200  19.877 108.429  0.50 32.58           C

HETATM18366  C06AUJM B1301      -5.027  17.825 110.133  0.50 31.64           C

HETATM18367  C07AUJM B1301      -6.136  18.797 110.502  0.50 32.44           C

HETATM18368  C08AUJM B1301      -6.405  19.771 109.357  0.50 34.12           C

HETATM18369  O01AUJM B1301      -4.772  22.201 108.497  0.50 30.85           O

HETATM18370  O03AUJM B1301      -3.216  20.883 109.410  0.50 35.44           O1-

HETATM18371  S05AUJM B1301      -4.377  18.249 108.495  0.50 29.52           S

HETATM18372  C02BUJP B1302      -4.324  21.167 108.876  0.31 33.43           C

HETATM18373  C04BUJP B1302      -5.334  20.003 108.712  0.31 32.97           C

HETATM18374  C06BUJP B1302      -5.399  17.805 110.268  0.31 31.16           C

HETATM18375  C07BUJP B1302      -4.356  17.742 109.183  0.31 32.66           C

HETATM18376  C08BUJP B1302      -4.618  18.801 108.125  0.31 30.79           C

HETATM18377  O01BUJP B1302      -4.720  22.265 108.413  0.31 30.37           O

HETATM18378  O03BUJP B1302      -3.227  20.957 109.434  0.31 34.00           O1-

HETATM18379  S05BUJP B1302      -6.135  19.451 110.283  0.31 35.84           S


-----------------------
John J. Tanner
Professor of Biochemistry and Chemistry
Associate Chair of Biochemistry
Department of Biochemistry
University of Missouri
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Email: tannerjj at missouri.edu<mailto:tannerjj at missouri.edu>
https://cafnrfaculty.missouri.edu/tannerlab/
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A


From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Pavel Afonine <pafonine at lbl.gov>
Date: Thursday, September 14, 2023 at 10:47 PM
To: Calvin N Steussy <csteussy at purdue.edu>, phenixbb at phenix-online.org <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] racemic ligand refinement
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On 9/14/23 21:09, Calvin N Steussy wrote:
All,

I need to refine a ligand that consists of two stereoisomers in my active site.  I have decent density and have created models for the r and s forms of the guest with separate cif files.  They have been fit independently into the active site density.  My questions are;
How to show these in the pdb file.  Separate chains?  Separate amino acids in a given chain?
How do I keep them from interacting with one another during refinement?
Creating an alt-position seems obvious but I'm not certain how to apply the different stereo restraints in that case.

I'm sure someone has solved this before but I can't seem to find that information.

Thanks,

Nic Steussy
Purdue University.




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