[phenixbb] ligand - protein close contact

Nikos Pinotsis n.pinotsis at mail.cryst.bbk.ac.uk
Tue Jun 6 12:22:04 PDT 2017

Dear all,

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
Birkbeck College
Malet Street
London WC1E 7HX
T: +44 (0)207 631 6827
F: +44 (0)207 631 6803
M: +44 (0)792 384 3593

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