Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5759 |
| PDBID: | 7ZFB |
| Chains: | M_E |
| Organism: | Lama glama, Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.08 |
| Reference: | 10.1016/j.cell.2022.05.014 |
| Antibody | |
| Antibody: | C1 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron BA.1 spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2; P0DTC2; P0DTC2; |
Sequence information
Antibody
Chain: M
Mutation: NULL
| >7ZFB_M|Chain A[auth M], B[auth N]|Nanobody C1|Lama glama (9844) QVQLVESGGGLVQPGGSLRLSCAASGFTNDFYSIAWFRQAPGKEREGVSWLSVSDNTPTYVDSVKDRFTISRHNANNTVYLQMNMLKPEDTAIYYCAAGRFAGRDTWPSSYDYWGQGTQVTVSSKHHHHHH |
Antigen
Chain: E
Mutation: G13D/S45L/S47P/S49F/K91N/N114K/G120S/S151N/T152K/E158A/Q167R/G170S/N175Y/Y179H
| >7ZFB_E|Chain C[auth E], L[auth F]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) HHHHHHTNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGKK |
Interaction
1、Solvent accessible surface areas (SASA) were calculated (Naccess V2.1.1) for each residue in antibody and antigen, respectively. The residues with SASA loss in binding of more than 1Å2 were classified as interacting residues.
Interacting residues (ΔSASA based)
| M: PHE31 TRP50 SER52 SER54 ASP55 THR57 THR59 TYR60 VAL61 ASP62 LYS65 ARG100 PHE101 ALA102 GLY103 ARG104 ASP105 THR106 TRP107 SER109 SER110 ASP112 E: TYR365 LEU368 TYR369 ASN370 LEU371 ALA372 PRO373 PHE374 PHE375 THR376 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 LYS386 GLY404 ASP405 VAL407 ARG408 GLN414 VAL503 GLY504 TYR508 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 5Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 5 Å from any atom.
Interacting residues (Atom distance based)
