[phenixbb] SSBOND for protein-ligand

Nigel Moriarty nwmoriarty at lbl.gov
Tue Jun 9 12:28:51 PDT 2020


As list admin, I saw the images in the "too big" post. Why do you want an
SSBOND record specifically in the PDB file? It's the mmCIF file that is
deposited for x-ray structures and I'd recommend for cryoEM also.



Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Tue, Jun 9, 2020 at 11:33 AM Wei Wang <ww2283 at columbia.edu> wrote:

> Dear all,
> I’m seeking help for establishing disulfide bond between protein and
> ligand. I used phenix.readyset to prepare the model for refinement then
> used phenix.elbow to generate the cif for ligand. After refinement, the
> sulfur from ligand, which was meant to be forming disulfide bond, is linked
> to the adjacent CYS by dashed line. I do see the LINK record in refined
> pdb. I tried manually add SSBOND record line in the pdb, following format
> instructions on wwpdb, but didn’t succeed. Thus I’m here looking for help
> on how to properly introduce disulfide bond between a ligand and cysteine.
> Some further explanation: When I display the readyset output in Pymol, the
> disulfide bond seems to be correctly recognized. I guess it’s because the
> sulfur atoms are within the detectable distance for a SSBOND. When I opened
> the same pdb in Coot, the disulfide bond is not present. I noticed a
> similar situation in PDB:6O9V, where the ligand M1M (chain B and resseq
> 401) was refined with LINK record but not SSBOND.
> (Sorry if this is a repeat message: previous message was put on hold
> because attachment pic size was too big.)
> Regards,
> Wei
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