On 12/09/14 23:28, Wang, Bing wrote:
Hi guys,
Hello.
A quick question about pdb deposition! My protein has a common ligand 'heme' which mismatches with the ligand in pdb CCD (/Chemical Component Dictionary/).
What makes you think so?
However i didn't find any differences in it. Is that because of the positions of double bonds or hydrogen atoms,
unlikely.
since my model don't have hydrogen atoms. Actually i replace the heme with exact one from CCD and run refmac which give me a new pdb file. Unfortunately, CCD still didn’t recognize the heme.
It is not clear to me what test you are performing. I do note that the SMILES for HEM in the CCD doesn't contain Fe - that might be related.
HTH, Paul.
