[modeller_usage] Missing residues in PDB file

[Szymon Żaczek <>]

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