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
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Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Tue, Jun 9, 2020 at 11:33 AM Wei Wang
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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