Question: Getting the interacting protein chains in a PDB file
gravatar for Reyhaneh
4.3 years ago by
United Kingdom
Reyhaneh480 wrote:


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:

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.


ADD COMMENTlink written 4.3 years ago by Reyhaneh480

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:

ADD REPLYlink written 4.3 years ago by genomax83k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1896 users visited in the last hour