Fig. 2: Homotypic Fab–Fab interactions in Fab239- and Fab399-peptide complexes.
a Two copies of Fab239 (Fab A, black: heavy chain, white: light chain. Fab B, dark brown: heavy chain, tan: light chain) in the crystal structure are shown as surfaces with the NPNA4 peptide represented as a yellow tube. b, c Interactions between two Fabs (A and B) that simultaneously recognize an NPNA4 peptide. Hydrogen bonds (yellow dashes) and salt bridges (black dashes) are highlighted. The Fabs are shown as cartoon representations with the side chains of interacting residues represented as sticks. CDRs as defined by Kabat are colored green, blue, magenta, light green, light cyan, and pink for CDR H1, H2, H3, L1, L2, and L3, respectively. d Surface representation of homotypic, head-to-head interactions of two copies of Fab399 in the crystal structure with NPNA6 peptide (yellow tube). e, f Contacts between two Fabs that simultaneously recognize the NPNA6 peptide (transparent yellow tube). All coloring schemes and representations are as for the Fab239-NPNA4 complex. g Individual residue contributions to the BSA of inter-Fab interactions are shown in a bar plot for the heavy and light chains of Fab239 and Fab399. The yellow and blue bars indicate the BSA on Fab A and Fab B (defined as in previous panels), respectively, while the green bars show the overlap of both. The CDRs are colored as in previous panels. Additionally, the alignment between the Fab heavy/light chain sequences and germline IGHV and IGKV gene sequences is shown to display somatically mutated residues. “H” and “S” mark residues that are engaged in hydrogen bonds and salt bridges, respectively. Antibody amino acid residues are labeled with a superscript “H” for heavy chain and “L” for light chain. Residue numbers are also shown as superscripts.
