Fig. 5.

Recognition of the parallel CCs GCN₂ and P5-P6 by nanobodies Nb39 and Nb34. (A) Complex between Nb39 (gray) and GCN₂ homodimer (brown). Nb39 interacts with both GCN chains using an extended CDR3 loop in a β-hairpin conformation extending from the nanobody framework. Additional contacts with the second GCN chain are provided by CDR1 and framework residues. CC N and C termini are marked with dots. Nanobody interactions (colors correspond to different CDR loops, while non-CDR interactions are shown in brown) are shown schematically on the CC surface lattice, with CC residues mediating hotspot interactions highlighted by red squares. (B) Complex between Nb34 (green) and P5-P6 heterodimer (orange). The majority of interactions with P5 (bright orange) and P6 (dark orange) are formed by the CDR2 loop and nanobody framework (non-CDR), with only limited contributions from CDR1 and CDR3 residues. Nanobody interactions with P5-P6 are shown schematically on the CC surface lattice (left lattice shows P5 residues, and the right one shows P6 residues).