Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7309 |
| PDBID: | 7OAQ |
| Chains: | A_B |
| Organism: | Lama glama, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 1.55 |
| 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: | Yes |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Chain: A
Mutation: NULL
| >7OAQ_A|Chain A[auth AAA]|H3|Lama glama (9844) QVQLVESGGGLVQPGGSLRLSCAASGFTNDFYSIAWFRQAPGKEREGVSWLSVSDNTPTYVDSVKDRFTISRHNANNTVYLQMNMLKPEDTAIYYCAAGRFAGRDTWPSSYDYWGQGTQVTVSSKHHHHHH |
Antigen
Chain: B
Mutation: N172Y
| >7OAQ_B|Chain B[auth EEE]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) PNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNKHHHHHH |
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 SER52 SER54 ASP55 THR57 PRO58 THR59 ARG100 PHE101 ALA102 GLY103 ARG104 ASP105 THR106 TRP107 SER109 SER110 ASP112 B: TYR40 ASN41 SER42 PHE45 SER46 THR47 PHE48 LYS49 CYS50 TYR51 GLY52 VAL53 SER54 PRO55 THR56 GLY75 ASP76 VAL78 ARG79 GLN85 VAL174 GLY175 TYR179 |
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)
