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>I had a question about flexibility in ligand binding in an enzyme active site. >Is it possible for a substrate/product analogue to bind in more than one conformation in the active site. Yes. It is even possible for portions of a ligand to be disordered and not discernable in electron density. >Since the ligand/enzyme interactions are very specific I am a little confused about this. >Also which program would you use if you have to refine with alternate ligand conformation. REFMAC will do this just fine. Just make sure you have the "A", "B" conformers set in the PDB file. EG: ATOM 72 CA APRO A 7 -2.619 28.983 -0.796 0.62 6.48 C ATOM 73 CA BPRO A 7 -2.226 29.044 -0.847 0.38 5.76 C