843509.fig.004a
(a)
843509.fig.004b
(b)
Figure 4: Ferric pyoverdine does not dock inside the NGAL calyx. (a) Docking of ferric pyoverdine (bound to iron) into the NGAL trimer crystal structure (PDB 1L6M) using AutoDock Vina. NGAL protein in red, blue, and green ribbon diagrams with nine positions of docked pyoverdine shown. For this illustration only one pyoverdine molecule is displayed in each of the predicted binding positions on the rigid NGAL. All simulated docking modes were on the surface and between the units of NGAL but not near or in the ligand-binding site. The binding affinity for each docking mode is listed in Table 1. (b) Ferric pyoverdine docking into the NGAL monomer crystal structure (PDB 1QQS) using AutoDock Vina. Modes 1–8 docked near the opening of the NGAL calyx without fully fitting in the hydrophobic pocket, while mode 9 docked on the opposite surface. The binding affinity for each docking mode is listed Table 1.