Figure 5

OptCDR predictions of antibody-peptide binding modes. The following coloring was used in each panel of this figure: the modeled peptide is in blue with the DYKD residues shown as stick structures, the heavy chain framework is dark gray with the heavy chain CDRs in orange, while the light chain framework is in light gray with the light chain CDRs in yellow. (A) An overlay of the three predicted antibody structures, EEh13.6, EEh14.3 and EEf15.4, with each CDR position highlighted. The CDR residue alignments are shown in Fig. 2A. (B–D) Show the key predicted interactions between DYKD and EEh13.6, EEh14.3 and EEf15.4, respectively, with each antibody in the same orientation as in panel (A). Each interaction incudes several predicted hydrogen bonds, shown as dashed black lines. In EEh13.6, the backbones of light chain residues S92 and L93 and heavy chain residue R58 are positioned to form hydrogen bonds with the P3 lysine and the backbone of the P2 tyrosine, respectively. In EEh14.3, all four peptide residues are predicted to form hydrogen bonds with antibody residues: heavy chain residue R58 interacts with the first peptide aspartic acid, the backbone of light chain residue G91 with the peptide tyrosine, the sidechain and backbone of heavy chain residues N95 and E96, respectively, with the peptide lysine and light chain residue Y32 with the backbone of the final peptide aspartic acid. In EEf15.4 and EEf154.a, heavy chain CDR3 residue R95 is positioned to hydrogen bond with the backbone of the peptide P2 tyrosine, and Y100a to form a hydrogen bond with the peptide P4 aspartic acid while CDR L1 residue E34 is predicted to form a hydrogen bond with the P3 lysine. The corresponding PDB files are available as supplementary datasets.