Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants
Fig 3
Distribution of antibody clusters on the receptor binding domain.
(A) Each antibody is represented as a sphere at the paratope center (centroid of all non-hydrogen atoms within 5 Å of the RBD), and colored by contact-based antibody cluster (1: blue, 2: green, 3: red, 4: magenta). A representative RBD structure (from PDB code 7KN5) is shown in gray, and the N-glycan at residue N343 from that structure is shown as orange sticks. (B) RBD structure with antibody clusters and superposed ACE2 receptor (tan cartoon; PDB code 6LZG [52]). (C) RBD antibody clusters shown in the context of the spike glycoprotein (light blue cartoon; PDB code 6VYB [68]) with the RBD in an open state. (D) Representative antibodies from each cluster, labeled by antibody name and colored by cluster, superposed onto the RBD.