Docking calculations on the binding interface between the Fab and the C-domain of P1.

a) Interface observed in the 2.3 Å resolution map. (b) Top-ranked model obtained from HADDOCK1 docking simulations performed with a lower resolution map, the P1 crystal structure and the AlphaFold2 prediction of the Fab. Docking models were ranked based on Haddock docking score (-66.44 arbitrary units), buried surface area (1457 Ų), and correlation with the cryo-EM map (0.85, as calculated with Chimera³). The C-domain of P1 is colored in green, the loop Val1425-Asp1438 in orange, and the heavy and light chains of the Fab in cyan and magenta, respectively. For clarity, only the variable fragment of the Fab is shown. (PDF)