Fig. 3

Structure of the NbALFA-ALFA peptide complex. a View on the NbALFA-ALFA peptide complex illustrated as cartoon (left) or surface representation (right). NbALFA: orange with CDRs 1–3 colored in yellow. ALFA peptide in blue. For both molecules, the N-terminal is oriented left, the C-terminal right. b Polar interactions within the N-terminal region of the ALFA peptide. ALFA peptide residues are denoted by an apostrophe. S2’ and E5’ form hydrogen bonds with CDR2 (S57, E58, R59 and N61). R3^’ reaches out to CDR3 and interacts with the backbone of V107 and the side chain of D105. c R3’ and E7’ sandwich F110 on the nanobody, forming a cation-Pi interaction (reviewed in ref. ⁵²). d Illustration of a hydrophobic cluster (L4’, L8’ and L12’) facing the nanobody’s hydrophobic cavity. e Polar interaction near the C-terminal of the ALFA peptide. The backbone of E14’ forms hydrogen bonds with R65 while the side chain of R11’ interacts with D112 and Y42 on the five-stranded β-sheet. Interestingly, Y42 has been described as a conserved residue in nanobodies of this particular architecture⁸