Figure 2

Examples illustrating the difficulty in defining a ligand. F16BPase tetramer (a) in free form ([PDB:2FBP]), (b) with F6P (red sphere) in the active site ([PDB:1RDX]), (c) with F6P and AMP (yellow sphere) in the allosteric site ([PDB:1FBP]), and (d) with F6P, AMP, and PFE (green sphere) in the non-native allosteric site ([PDB:1KZ8]). Although [PDB:1RDX] is in a ligand-bound state against [PDB:2FBP], it is also in a ligand-unbound states against [PDB:1FBP]. Further, although [PDB:1FBP] is in a ligand-bound state against [PDB:2FBP] and [PDB:1RDX], it is also in a ligand-unbound state against [PDB:1KZ8]. If a ligand is defined specifically as "HETATM molecules except for low-molecular ions," all entries but [PDB:2FBP] are obtained in a ligand-bound state. The flexible ligand definition in the BUDDY-system enables the user to obtain all possible ligand-bound and unbound states pairs of F16BPase.