[phenixbb] racemic ligand refinement
Tanner, John J.
TannerJJ at missouri.edu
Fri Sep 15 13:17:40 PDT 2023
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
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Phone: 573-884-1280
Email: tannerjj at missouri.edu<mailto:tannerjj at missouri.edu>
https://cafnrfaculty.missouri.edu/tannerlab/
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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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