Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7317 |
| PDBID: | 7OLZ |
| Chains: | B_A |
| Organism: | Vicugna pacos, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 1.75 |
| Reference: | 10.15252/embj.2021107985 |
| Antibody | |
| Antibody: | Re9F06 VHH |
| 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: B
Mutation: NULL
| >7OLZ_B|Chain B|Nanobody Re9F06|Vicugna pacos (30538) GSQVQLVESGGGLVQAGGSLRLSCAASGRTFSNDALGWFRQAPRKEREFVAAINWNSGTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYSCAAASDYGLPREDFLYDYWGQGTQVTVSSTS |
Antigen
Chain: A
Mutation: NULL
| >7OLZ_A|Chain C[auth A]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP |
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: ASN52 TRP53 ASN54 GLY56 SER99 ASP100 TYR101 GLY102 LEU103 PRO104 ARG105 GLU106 ASP107 PHE108 LEU109 TYR110 ASP111 A: LEU368 TYR369 SER371 ALA372 SER373 PHE374 SER375 THR376 PHE377 LYS378 CYS379 SER383 GLY404 ASP405 VAL407 ARG408 ASN437 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)
