I have a protein that forms a dimer and the dimer has a groove that we hypothesize is used for binding a ligand or small molecule. I want to run the structure through a database to see if it get's any hits but everything I've found that accepts .pdb files won't accept the protein as the dimer >500 sequences (750) and everything that accepts the FASTA sequence doesn't have an option to enter both sequences to check against the dimer.
I need some sort of idea as to what will bind so I can narrow down my criteria and start some in-vitro binding assays.
Any and all suggestions would be greatly appreciated.
Here's the link to the .pdb of the protein if that helps.