[phenixbb] SSBOND for protein-ligand

[Wei Wang]

Hi Nigel,

Thanks for pointing out the mmCIF issue, which clearly skipped my mind. My main concern is this interaction should be better be shown as a covalent connection. That’s why I’m looking for the possibility of modeling it as the normal Cys-Cys connection. Another reason is that I always get a bond forming between the sulfur and one carbon of the ligand in itself, even though the cif from phenix.elbow was supplied. I felt if the bond between Cys-ligand was correctly established maybe this intra-molecule bond problem can be solved…

Regards,

Wei




> On Jun 9, 2020, at 3:28 PM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:
> 
> Wei
> 
> 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.
> 
> Cheers
> 
> Nigel
> 
> ---
> 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 <http://cci.lbl.gov/>
> 
> On Tue, Jun 9, 2020 at 11:33 AM Wei Wang <ww2283 at columbia.edu <mailto: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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