Superimposition of six crystal structures of BACE1. Only the bound ligand and the three loops including residues 5–16, 67–77 and 105–117 are shown. (a) The BSIIV complex obtained by cocrystallization (green), the BSIIV complex obtained by soaking (cyan) and the previously deposited BSIIV–BACE1 structure, also obtained by soaking (PDB entry 2b8l; yellow). (b) Apo enzymes: Apo1 structure (magenta), Apo2 structure (purple) and the previously deposited apo structure of BACE1 (PDB entry 1w50; light pink). (c) Superimposition of the six structures shown in (a) and (b).