Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7307 |
| PDBID: | 7OAP |
| Chains: | A_B |
| Organism: | Lama glama, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 1.90 |
| Reference: | 10.1038/s41467-021-25480-z |
| Antibody | |
| Antibody: | C1 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Chain: A
Mutation: NULL
| >7OAP_A|Chain A[auth AAA]|C1 nanobody|Lama glama (9844) QVQLVESGGGLVQPGGSLRLSCAASGFTNDFYSIAWFRQAPGKEREGVSWLSVSDNTPTYVDSVKDRFTISRHNANNTVYLQMNMLKPEDTAIYYCAAGRFAGRDTWPSSYDYWGQGTQVTVSSKHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >7OAP_B|Chain B[auth EEE]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) NITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNKHHHHHH |
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)
| A: PHE31 TRP50 SER52 SER54 ASP55 THR57 THR59 ARG100 PHE101 ALA102 GLY103 ARG104 ASP105 THR106 TRP107 SER109 SER110 ASP112 B: TYR39 ASN40 SER41 PHE44 SER45 THR46 PHE47 LYS48 CYS49 TYR50 GLY51 VAL52 SER53 PRO54 THR55 GLY74 ASP75 VAL77 ARG78 GLN84 VAL173 GLY174 TYR178 |
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)
