Getting the interacting protein chains in a PDB file
Hi
I am trying to write a script which automatically picks the subunits for a protein complex. Instead of the PDB I am using the IMGT format which is just different numbering system.
For example for 1KJ3, we have: http://www.imgt.org/3Dstructure-DB/cgi/details.cgi?pdbcode=1KJ3&Part=File
By looking at the 1KJ3 you can see there are two similar subunits where chains (Q,I,M) and (P,H,L) interact. What is the best way to get this information directly from the PDB file without needing to look at the structures? Should I calculate distances among chains?
FYI I am using Python & BioPython.
Thanks
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If I understand you question right what you are looking for is information about "biological assemblies" if that is what you mean by interacting protein chains. That information is in the PDB file (and may also be in the IMGT format, I am not familiar with that). See the tutorial here: http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies