Hi all-
The MODELLER documentation at https://salilab.org/modeller/manual/node149.html#MEMB:iodata.convertmodres says the following:
"Some special handling is done for certain commonly-used modified residues. The MSE residue type is mapped to the regular MET amino acid, and the SE atom in this residue is mapped to SD. The MEX and ABU residue types are both mapped to CYS."
According to https://salilab.org/archives/modeller_usage/2003/msg00051.html the reason for this is that MEX is "cysteine bridged with beta-mercaptoethanol".
I recently encountered PDB ID 3OW6. This structure includes a ligand labeled MEX. The ligand does not resemble CYS, and the presence of MEX causes an error. I'm reluctant to set io_data.convert_modres to False, because I'd like to handle other modified residues (ex. MSE).
I was able to work around the issue, so it didn't impact me too much. But I thought I should say something in case others run into the same issue. I see that the ligand CME does resemble CYS, with beta-mercaptoethanol attached through a disulfide bond. Is it possible that MEX and CME are switched?
Best, Daniel Evans
On 2/1/20 10:58 AM, Daniel Evans wrote: > The MODELLER documentation at > https://salilab.org/modeller/manual/node149.html#MEMB:iodata.convertmodres > says the following: > > "/Some special handling is done for certain commonly-used modified > residues. The MSE residue type is mapped to the regular MET amino > acid, and the SE atom in this residue is mapped to SD. The MEX and > ABU residue types are both mapped to CYS./"
... > I recently encountered PDB ID 3OW6. This structure includes a ligand > labeled MEX. The ligand does not resemble CYS, and the presence of MEX > causes an error. I'm reluctant to set io_data.convert_modres to False, > because I'd like to handle other modified residues (ex. MSE).
This part of the Modeller code is ancient, at least 15 years old, and PDB has changed a lot since then. I don't see any examples of MEX used as a polymer in current PDB (and only 1 example of it used as a ligand, in 3ow6 as you noted) and only 3 examples of ABU polymer. Since neither MEX nor ABU look much like CYS, I will remove this code entirely from the next Modeller release - they can't be considered "commonly-used modified residues" and it is probably causing more harm than good. (Of course, if anybody relies on this ABU/MEX->CYS mapping, 1. it is easy to work around and 2. let me know!)
Ben Webb, Modeller Caretaker
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Daniel Evans -
Modeller Caretaker