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?
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written
by
rein07 •
2 answers
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
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.
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