Fig. 6

Binding poses elucidated from molecular docking. a, b Most energetically favorable binding poses from flexible molecular docking of Xa in two of the top-ranked binding pockets in crystallin. In each panel, the figures on the left show the orientation and size of the pigment molecule (space-filling beads) within the binding pockets of the respective proteins (cartoons colored by secondary structure). The inset provides closeup views of the molecule within the pockets. The figures on the right are schematics of the pigment molecule interacting with the amino acid sidechains in the respective pockets. Dotted lines indicate polar interactions between acceptor–donor pairs. Eyelashes (in red) denote sidechains and atoms that are in contact with each other. Solid circles represent carbon (black), oxygen (red), nitrogen (blue), and sulfur (yellow). c Top and side views of the five top-ranked poses of Xa binding from rigid docking (space-filling beads) within the central cavity of the crystallin tetramer (cartoon colored by chain number), where the five molecules are in disparate regions of the cavity. Inset provides a closeup view of these poses. Top and side views of the tetramer’s molecular electrostatic potential map are shown at the bottom