Antibody Recognition of Cancer-Related Gangliosides and Their Mimics Investigated Using in silico Site Mapping
Figure 3
Evaluation of site mapping using high resolution crystal structure complexes.
Kdoα(2→4)Kdoα(2→4)Kdoα(2-OAll) binding to S73-2 (PDB 3HZY) described by hydrogen bonding map (A) and van der Waals interaction map (B). Kdoα(2→8)Kdoα(2→4)Kdoα(2-OAll) binding to S25-39 (PDB 3OKO) described by hydrogen bonding map (C) and van der Waals interaction map (D). The color depth indicates the level of involvement of a particular residue in ligand recognition; more strongly illuminated residues are more involved in ligand recognition than weakly illuminated residues. The crystal structure binding mode is shown in each structure in sticks colored by atom type (C, yellow; O, red). Images rendered using PyMOL [64].