[phenixbb] ligand - protein close contact
Tanner, John J.
TannerJJ at missouri.edu
Tue Jun 6 12:36:11 PDT 2017
I had a similar problem in Feb. 2017 with a sulfate ion running into a flavin. It turned out the PDB file mistakenly had a “LINK” line forcing a covalent bond where there should not have been one. I deleted the LINK line from the PDB file and everything was fine.
I think Pavel looked into the automatic linking algorithm with my files but I never heard of a resolution to the issue.
John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Email: tannerjj at missouri.edu<mailto:tannerjj at missouri.edu>
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On Jun 6, 2017, at 2:22 PM, Nikos Pinotsis <n.pinotsis at mail.cryst.bbk.ac.uk<mailto:n.pinotsis at mail.cryst.bbk.ac.uk>> wrote:
I have a protein-ligand structure with several chains in the AU. After refinement one of the ligands forms a close contact 1.8A with the protein. For the rest of the protein-ligand chains the same interaction is as expected to 2.7-2.8 A forming an H-bond. I tried to adjust this ligand with coot but everytime I am getting back the same 1.8 A close contact. There is enough density for the ligand and I can even see that it can fit better to distance 2.4-2.5A H-bond with the protein
Is there a way to constrain this distance to more than 2A? Should I fix the ligand atom that interacts? Unless I am missing something more fundamental. The ligand cif file is the default in phenix, the data set is a quite decent 2.3A.
thanks in advance for any suggestions
Dr. Nikos Pinotsis
Institute of Structural and Molecular Biology
Department of Biological Sciences, 3rd Floor, R313
London WC1E 7HX
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