For some benchmarks I am looking for information about proteins with several binding sites (at least two) where, depending on the ligand, they interact on different binding sites. I am looking firstly for protein structures, which are available at PDB Database, but could not find relevant information there, could you recommend other databases?
We searched the PDB for protein structures with 2 or more ligands. Then I'd just curate the ligands to make sure they are different and calculate centers of mass to make sure they are binding to different spots. Also, you could look for proteins binding ONE ligand and then cross-reference this set to find multiple ligands bound to the same protein.
Seriously, this is really easy to do, it's a matter of searching the PDB appropriately.