Fig. 1: Analysis of Antibody-Framework-to-Antigen Distance (AFAD) for all antibody complexes in the PDB reveals outliers with extended recognition distances to be exclusively HIV-1 broadly neutralizing antibodies.

a Schematic of AFAD calculated from the shortest protein antigen atom-distance to each of the four conserved variable domain cysteines (red). Only protein atoms were used for calculations, excluding distances for cofactors, glycans, and other non-protein atoms. b Histogram of AFAD for n = 1879 antibody complexes in the PDB (black). Normalized AFADs relative to mean are also shown for Ebola virus (blue), SARS-CoV-2 (purple), influenza A virus (green), Dengue/Zika virus (yellow), human immunodeficiency virus-1 (HIV-1) non-broadly neutralizing antibodies (gray), and broadly neutralizing antibodies targeting HIV-1 (red). AFAD relative to mean for n = 1879 PDB complexes formed a normal distribution as mean values 16.3 +/− 2.4 Å SD. Select HIV-1 broad neutralizing antibody-recognition distances can be extended by more than 3σ longer. AFADs in the bottom plot are normalized relative to mean (16.3 Å). See also Supplementary Table 1.