Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7312 |
| PDBID: | 7OAY |
| Chains: | B_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.34 |
| Reference: | 10.1038/s41467-021-25480-z |
| Antibody | |
| Antibody: | F2 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >7OAY_B|Chain B[auth BBB], D[auth DDD], F[auth FFF], H[auth HHH], J[auth JJJ], L[auth LLL]|F2 nanobody|Lama glama (9844) QVQLVESGGGLVQAGGSLRLACIASGRTFHSYVMAWFRQAPGKEREFVAAISWSSTPTYYGESVKGRFTISRDNAKNTVYLQMNRLKPEDTAVYFCAADRGESYYYTRPTEYEFWGQGTQVTVSSKHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >7OAY_A|Chain A[auth AAA], C[auth CCC], E[auth EEE], G[auth GGG], I[auth III], K[auth KKK]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) PNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNKHHHHHH |
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)
| B: SER52 TRP53 PRO57 TYR59 ASP99 ARG100 GLY101 GLU102 SER103 TYR104 TYR105 ARG108 THR110 GLU111 GLU113 A: LEU39 TYR40 SER42 ALA43 PHE45 SER46 THR47 PHE48 LYS49 CYS50 TYR51 GLY52 VAL53 SER54 PRO55 THR56 ARG79 PRO83 GLN85 ASP98 |
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)
