Dear Bing Wang,
To solve your problem, you may try to take a eme ligand directly from a
PDB that contains it, e.g. 1HRC.
You should download the PDB file and to copy and paste the ligand
coordinates in a new file and then use this new pdb file to refine your
structure.
It could be a good solution.
Danilo
Il 2014-09-13 00:28 Wang, Bing ha scritto:
> Hi guys,
>
> A quick question about pdb deposition! My protein has a common ligand
> 'heme' which mismatches with the ligand in pdb CCD (_Chemical
> Component Dictionary_). However i didn't find any differences in it.
> Is that because of the positions of double bonds or hydrogen atoms,
> 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.
>
> Solutions?
>
> Thank you!!
>
> Bing Wang
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