Superposition of antibody 13G5 in its unliganded state (gray) and in complex with hapten 5 (blue). Only minor adjustments take place at the mouth of the binding pocket, showing that the antibody does not undergo major remodeling upon ligand binding.

Electrostatic and shape complementarity of the hapten to the 13G5 antibody combining site. A slice through the center of the binding site is shown. The electrostatic potential was calculated in APBS (43) and mapped onto the surface with the color code ranging from -30 kT/e (bright red) to + 30 kT/e (dark blue). The base of the pocket has strongly negative electrostatic potential due to the two carboxylic acids, Asp^H35 and Glu^L34. The architecture of the binding pocket reveals the structural basis for the observed substrate specificity.

Antibody combining site of 13G5 wild-type (A), Glu^L34Gln mutant (B), and Glu^L34Ala mutant (C) bound to its hapten. The light and heavy chains are colored in green and blue, respectively. The σ_a-weighted difference F_o-F_c electron density maps (pink mesh) were calculated by omitting the ligand and active site water molecules and are contoured around the ligand at 3.0σ. The σ_a-weighted 2F_o-F_c electron density map (blue mesh) is contoured at 1.4σ. Hydrogen-bonding interactions of 13G5 wild-type (D), Glu^L34Gln mutant (E), and Glu^L34Ala mutant (F) with hapten 5. The proton-abstracting Asp^H35 makes a bidentate hydrogen-bond interaction with the gunanidinium group of the hapten. While only slight variations are observed in the Glu^L34Gln mutant to the wild-type, the immediate environment around the proton-donating water molecule W5 in the Glu^L34Ala mutant shows a marked difference in the solvent structure.