Structural Analysis of ClfB Protein

ClfB structures were downloaded from the Protein Data Bank (34 (link)). The structures for ClfB, PDB ID 4F20, 4F1Z and 4F27, were used (15 (link)). ClfB structures and their ligands were superposed using the align/superpose function in the Molecular Operating Environment (Chemical Computing Group, Montreal, Canada). All ligands studied were prepared for docking using the “wash” function and all tautomers enumerated. CCPDB structures, 4F20 (ClfB) (15 (link)) and 2VR3 (ClfA) (13 (link)) were used as the targets and prepared for docking using the protonate 3D function with default parameters. The peptide ligand was used to define the binding site for docking using macromolecule residues within 4.5 Å of the peptide ligand. Docking was performed using the Triangle Matcher function for placement and London delta G scoring, storing 30 poses. Rigid receptor was used for refinement and GBVI/WSA delta G scoring for the final poses.