Biolip: pocket - chain relationship

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Biolip: pocket - chain relationship

Post by yaron »

Dear colleagues,

I wanted to ask regarding pockets of multi chain proteins - as far as I understand, pockets are not limited to a particular chain in a multi chain protein complex. For example pockets may be defined as the set of atoms on the protein that are less than a threshold (6A) from one of the ligand's atoms, regardless of which chain holds these protein atoms.

However, as far as I understand, Biolip is organized in a way in which there is a relationship between the particular protein chain and the ligand.

For example pdb_id 8stw has 2 binding sites for its A chain, one for ligand HEM and one for PLP.
However it has 10 additional binding sites on chains B through F on the same PLP and HEM ligands.

Can you please point me to information that can help me clarify this pocket - chain relationship?