Zhanglab forum

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?

Thanks!

8stw is a homo-hexamer, where each chain binds to one PLP and one HEM. Therefore, the full biological assembly has 6 different PLP and 6 different HEM ligands for the 6 different chains. Therefore, it is not true that the same ligand binds to 6 different chains simultaneously.

Thank you for your reply.
How do you view something like 3E90 where 2 chains are near the same ligand? (A and B are near the same ligand, while C and D are near another instance of a ligand)

Thanks!