Binding mode of aDabi-Fab and conformational differences between apo and holo structure. (A) Binding site of aDabi-Fab in complex with dabigatran (the respective electron density of dabigatran is shown in pale cyan, contoured at 1.5 sigma). The benzamidine group of dabigatran (carbon atoms colored in gray) extends into a cavity formed by the interface of light (light ochre) and heavy chain (dark ocre). It forms a bidentate salt bridge to H:Asp35 and additional hydrogen bonds to L:His96 and H:Asp100D, respectively (indicated as green dotted lines). The amine nitrogen of dabigatran forms a nonclassical H-bond to L:Tyr32. L:Tyr27D interacts with the benzimidazole moiety of dabigatran via parallel displaced π-stacking. H:Tyr100C forms a hydrogen bond to the aldimine nitrogen. H:Trp52 forms two T-shaped aromatic interactions with the benzamidine and pyridine moiety of dabigatran, respectively. (B) Superposition of the binding site of aDabi-Fab in its apo conformation and bound to dabigatran (color scheme as in Figure 4, the apo structure is colored in pale cyan). The orientation of the sidechain of H:Tyr100C changes by 3.2 Å (hydroxyl oxygen) upon binding of dabigatran, which causes the apex of CDR:H3 to increase its relative distance to the binding site by 2.1 Å (measured from the Cα of H:Tyr100). About the same distance CDR:H2 moves toward the binding site (measured from the Cα of H:Gly55) and the H:Trp52 and L:Phe94 adopt different side chain conformations. This concerted movement opens the binding site of dabigatran.