Question: Extract protein complex structures from pdb database
0
gravatar for Pappu
4.8 years ago by
Pappu1.9k
Pappu1.9k wrote:

I have a protein sequence with known structure. I want to download all the pdb structures of the protein in complex with other proteins. I am not sure how it can be done. Thanks.

pdb • 2.2k views
ADD COMMENTlink modified 4.5 years ago by CikLa90 • written 4.8 years ago by Pappu1.9k

Do you have the list of PDB ID's that this protein is in, or is that what you are trying to find?  PDB files of complexes will show the other protein(s) as separate chains, so you would just need to extract the coordinates for the other chain(s) in the PDB file.

ADD REPLYlink written 4.8 years ago by alolex910

I am trying to find the pdb ids.

ADD REPLYlink written 4.8 years ago by Pappu1.9k

Take your protein sequence and use BLAST to align it to all sequences in the PDB.  The database option of BLAST will give you the PDB database option.  If there are any this should pull them up for you.

ADD REPLYlink written 4.8 years ago by alolex910

If you have id of your protein like uniprot id then you can submit it into PDB search box and  you will get all structures (bound or unbound) related to your protein. Then download those structures from PDB and open file to look how many molecules present in each pdb file and any of them is related to protein or not excluding your own protein. Best way to right script to extract those information if you have too many files.

ADD REPLYlink written 4.8 years ago by Pallab Bhowmick20
1
gravatar for CikLa
4.5 years ago by
CikLa90
Malaysia
CikLa90 wrote:

Hi,

Let say for this one: http://www.rcsb.org/pdb/explore/explore.do?structureId=3PTA

Is it means that the protein of DNMT1 is bound to DNA molecule? And is the polymer number there (3) is indicating how many structures are there? So, in this case, the number of polymer is stated as 3, meaning that one is protein, and another 2 are for DNA? Is it the correct way of saying the PDB entry?

ADD COMMENTlink written 4.5 years ago by CikLa90
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