Biology Forums - Study Force

Hello,
I am not a biology major but I am taking a course in the field. I AM LOST :'(

So in this homework I am supposed to find the binding partners of a protein.

The database I am using is pdb.org, which gets me more information about the protein. Now how can I go about finding the binding sites and how can I view them in Jmol?

I would appreciate anyone who can help. I have already viewed the protein in Jmol, but I feel that what I am doing afterward is completely wrong.

HI

Do you have a specific protein in mind? Let us know.

my protein is ACBP which is DBI in human.
I will walk through the process in which I reached the entery in pdb.org

First I selected a isofrom that I want to analyze. Got the protein sequece for it and used Blast again (protein data base) from which I got the conserved domains for the gene. I chose the broadest domain and from which I got two pdb id numbers:


for your reference:
http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?ascbin=8&maxaln=10&seltype=2&uid=238248 (http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?ascbin=8&maxaln=10&seltype=2&uid=238248)

Now I got the acyl-CoA and CoA, which I suppose are the two different binding sites.. I think I am supposed to get three.

Then I visualize them using JMol. Are those:"acyl-CoA and CoA" the binding sites?

1) http://www.ebi.ac.uk/interpro/entry/IPR000582 (http://www.ebi.ac.uk/interpro/entry/IPR000582)

2) http://europepmc.org/abstract/MED/11491287 (http://europepmc.org/abstract/MED/11491287)