Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5738 |
| PDBID: | 7ZF4 |
| Chains: | F_E |
| Organism: | Lama glama, Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 4.18 |
| Reference: | 10.1016/j.cell.2022.05.014 |
| Antibody | |
| Antibody: | F2 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; |
Sequence information
Antibody
Chain: F
Mutation: NULL
| >7ZF4_F|Chain A[auth F]|Nanobody F2|Lama glama (9844) QVQLVESGGGLVQAGGSLRLACIASGRTFHSYVMAWFRQAPGKEREFVAAISWSSTPTYYGESVKGRFTISRDNAKNTVYLQMNRLKPEDTAVYFCAADRGESYYYTRPTEYEFWGQGTQVTVSSKHHHHHH |
Antigen
Chain: E
Mutation: G13D/S45L/S47P/S49F/K91N/N114K/G120S/S151N/T152K/E158A/Q167R/G170S/N175Y/Y179H
| >7ZF4_E|Chain D[auth E]|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)
| F: TRP53 SER54 THR56 PRO57 TYR59 ASP99 ARG100 GLY101 GLU102 SER103 TYR104 TYR105 ARG108 THR110 GLU111 GLU113 E: TYR369 ASN370 PHE374 PHE375 THR376 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 LYS386 PRO412 GLY413 GLN414 ASP427 ASP428 PHE429 |
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)
