Cryo-EM structure of POmAb bound to prothrombin. (A) Fab fragment of POmAb comprising heavy (purple; heavy [HC] and VH) and light (violet; light [LC] and VL) chains bound to kringle-1 (cyan). (B) Interacting surfaces of kringle-1 (top) and Fab (bottom) colored according to the electrostatic potential (blue = electropositive, red = electronegative). Note how residue R90 in kringle-1 is attracted by residue D314 of the antibody, resulting in electrostatic complementarity. Hydrophobic/hydrophilic interactions are mediated by Y93 in kringle-1 and a cluster of tyrosine residues (Y92, Y248, Y250, and Y274), and in the antibody, they provide additional binding energy. (C) Zoom-in of the binding interface between kringle-1 (cyan) and POmAb (purple). Shown are energetically favorable interactions between the 2 proteins. Antibody residues are shown in wheat. (D) Crystal structure of the closed form of prothrombin solved at 4.1-Å resolution (6C2W.pdb; yellow) overlayed on the 3.2-Å cryo-EM structure of the POmAb/kringle-1 complex shows how the protease domain clashes against the antibody. Binding of the protease domain and POmAb to residues R90-Y93 of kringle-1 is mutually exclusive.