Dear all,
I'm going to deposit to the PDB a structure in which a polypetidic chain
is made up by the fusion of two portions of proteins.
That is, it is a chimera of two proteins (say aa 1-100 of protein X
fused to aa 50-150 of protein Y)
Currently, this polypetidic chain has got a single chain ID and I've
kept residue numbers growing without caring about the original residue
numbers of the second protein (i.e. the chain A goes from residue 1 to
100, then 101 to 201 correspond to residues 50-150 of protein Y)
Now, I've always found it nice to have the correct numbering on the
residues, when I download a pdb, and was wondering if any of you could
suggest me a way to have this in my structure.
I wouldn't like to change the chain ID, a) beacuse what's crystallized
was a single polypeptidic chain b) because many programs will not put a
link between residues with different chain IDs
A solution would be adding something like "1000" to the numbers of the
residues of the second protein, but then again the residues numbers will
jump from 100 to 1050 and there will be no link created by some programs
(isn't it?)...
How could I do? Any suggestion is warmly welcomed!
Thanks in advance for the help,
Sebastiano
--
Sebastiano Pasqualato, PhD
IFOM-IEO Campus
Dipartimento di Oncologia Sperimentale
Istituto Europeo di Oncologia
via Adamello, 16
20139 Milano
Italy
tel +39 02 9437 5094
fax +39 02 574 303 310
