Figure 2. (A) The β-strand core region, the active site and the InsP₆ binding site together with the β-flap are conserved and align well for CPD’s of RTX_VC (gray), TcdA (green) and TcdB (blue). Shown are the crystal structures with the PDB-codes 3EEB (RTX_VC), 3OH6 (TcdA) and 3PA8 (TcdB). They all have InsP₆ bound and the substrate is cleaved. Therefore, there are no peptides bound in the active site (we refer to these structures as short). In TcdB the shown residues represent: C698, H653, D587, E743 and W761. (B) Re-docking of InsP₆ to the crystal structures of RTX_VC (3EEB), TcdA (3HO6) and TcdB (3PA8) with Autodock (blue) shows excellent agreement with the original position of InsP₆ (green). (C) β-flap movement of the InsP₆ free TcdA CPD (short form 3HO6) during a MD-simulation. Shown residues are C700, H655, D589, E745 and W763. (D) Along with the β-flap the Asp (D589) and His (H655) in the catalytic triad move drastically during an InsP₆ free MD-simulation of TcdA CPD (3HO6). Different snapshots at 3.5, 4.0, 5.0, 5.5 and 7.0 ns are compared with the crystal structure positions (green).