On Tue, Jul 11, 2017 at 11:26 AM, Szymon Żaczek <szymonzaczek@gmail.com> wrote:

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.

The numbering in the PDB files is messy. In order to preserve the numbering with the literature (so if residue 700 is interesting, all the papers will use the same number), they may skip some numbers or add variations (like 499A). You may also need to mutate the structure in order to crystallise it, or you won't see some other residues.

Your best bet to complete it is to align the sequence provided by the PDB (http://www.rcsb.org/pdb/download/viewFastaFiles.do?structureIdList=4ZA7&compressionType=uncompressed) to the sequence extracted from the structure, see if you have gaps, and model them.

/David.