 |
 |
1. what is the 3-letter code (residue type) of your heme? Ligand Explorer shows maybe half a dozen ligands for heme. Most notable HEM (protoporphrin 9 with Fe), HEC (same but with the double bonds in the vinyl substituents saturated) and HEA (heme a). There is even an entry for the trypanosomal/Eugenoid heme c with only one vinyl saturated. 2. What do you mean by "mismatches with the ligand in pdb CCD" and "CCD still didn’t recognize the heme" My understanding is that the 3-letter code defines the ligand, i.e. you could take acetate and rename it as HEM and it would be recognized as heme (with a lot of missing atoms and 4 additional ones). eab On 09/12/2014 06:28 PM, Wang, Bing wrote: > 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