Hi, anyone can please tell me is crystal structure of p50-p50 dimer (P-P) available?
I am able to find only p50 homodimer complexed to DNA on PDB site.
I need to do docking with its 10 bp binding site.
Please help.
p50 is not a very informative name. To find all related structures in the pdb, do a blast search with the sequence of the protein (https://www.rcsb.org/pdb/search/advSearch.do?search=new , scroll down to sequence: Blast/PSI-Blast and enter the sequence of your protein.
If you only see the monomer in the asymmetric unit, also look at the biological unit, as the dimer symmetry may coincide with the crystallographic symmetry.
If you already have the structure of the DNA complex, you can simply delete the DNA from the complex to get a free binding site for docking. You may need to dock the two monomers separately to the DNA.
If you have the structure of the DNA complex, first delete the DNA from the complex to get the homodimer structure.
then you delete another monomer to get a single monomer.
Then you have to dock the two monomers separately to form the homodimer by specifying the binding site.
then again you have to perform a docking separately with DNA specifying it's 10 bp binding site to form a homodimer-DNA complex.
All the best.
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