Hello,
I would like to perform a research on 4za7 protein. As long as using Modeller to insert missing residues is rather straightforward, the issue I have encountered is more related to PDB file itself. In the remark 465 section in the original pdb file, there are listed several missing residues:
REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ALA A 3 REMARK 465 ASN A 499A REMARK 465 LEU A 499B REMARK 465 GLU A 499C REMARK 465 HIS A 506 REMARK 465 HIS A 507
The problem is that I lack the knowledge on how to deal with those residues: 499A, 499B, 499C. I would most likely just insert 499A into the structure that will be further analysed but in regular residues that are normally placed in pdb file there is already a residue numbered 499. For some reason though, there are no residues 500 and 501 in the pdb file.
How should I proceed with it? Should I just ignore those different options for residue number 499 and go with the one that was properly determined by X-ray experiment, or should I do something else? Any suggestions from more experienced researchers will be welcome.
Kind regards, Szymon Zaczek