Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4848 |
| PDBID: | 7S83 |
| Chains: | B_C |
| Organism: | Ginglymostoma cirratum, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 2.52 |
| Reference: | 10.1038/s41467-023-36106-x |
| Antibody | |
| Antibody: | ShAb02 variable new antigen receptor (VNAR) 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
| >7S83_B|Chain A[auth B]|ShAb02 VNAR|Ginglymostoma cirratum (7801) ARVDQTPQTITKETGESLTINCVLRDSNCALASTDWYRKKSGSTNEESISKGGRYVETVNSGSKSFSLRINDLTVEDSGTYRCNAWDSWETRQLKCDYDVYGGGTVVTVNGPLEVLFQGPHHHHHHHH |
Antigen
Chain: C
Mutation: NULL
| >7S83_C|Chain B[auth C]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) NITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPGSHHHHHH |
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: ALA30 LEU31 ALA32 SER33 ASP35 TYR37 SER48 ILE49 SER50 LYS51 GLY52 THR58 VAL59 ASN60 SER61 GLY62 ASN84 TRP86 ASP87 SER88 TRP89 GLU90 THR91 ARG92 ASP97 ASP99 TYR101 C: ARG346 PHE347 ALA348 SER349 TYR351 ALA352 TRP353 ASN354 ARG355 LYS356 ARG357 TYR396 LYS444 GLY447 ASN448 TYR449 ASN450 LEU452 PHE464 ARG466 ILE468 SER469 THR470 GLU471 PHE490 |
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)
