How To Obtain All The Binding Sites/Pockets Of A Specific Protein By Providing The Pdb Id?

Question

[rein07]

Hi all.

I would like to find all the binding site and ligand of specific protein.

I already know the PDB ID of the protein and I have played around it on the PDB.

Yet I still can find and fields talking about the binding site or pocket of the protein.

Is it not included in the PDB?

Answer 1

[Woa]

The PDBSUM database can help you. If you have the ligand-bound protein structure, you can find that particular ligand binding site by the simplest approach: selecting all protein atoms within K angstrom of all ligand atoms. K is typically 7 to 8 Angstroms.

You can also have a look here http://bindingmoad.org/moad/welcome.do

[k8]

Why is it 7 to 8 Angstroms typically?

Answer 2

[Lukas Pravda]

PDBSUM is a good option, however it depends on which kind of binding sites you are focused on. If you are looking for a catalytic active sites, I would suggest you the CSA database. Nevertheless, ligand binding information is also directly by included in a pdb file. The record you are looking for is SITE and its description is given in REMARK 800.