Hi Bing, This is the result of the new PDB deposition system being buggy. I had a similar problem with imidazole recently. This is the solution given to me by the PDB annotators.
>Please choose from the instance page: >type of ligand: heterogen, >then give alternate ligand ID as IMD, (in your case HEM) >then click finish button address the issue. >It should solve the problem, if not, please let us know. Hope this helps, Katherine On Mon, Sep 15, 2014 at 3:03 PM, Wang, Bing <bingw...@ou.edu> wrote: > Forgot the picture! Here is it! > > ________________________________________ > From: Paul Emsley [pems...@mrc-lmb.cam.ac.uk] > Sent: Sunday, September 14, 2014 6:16 PM > To: Wang, Bing > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] ligand mismathces in pdb deposit > > 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. > > > -- "Nil illegitimo carborundum"* - *Didactylos
