Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5521 |
| PDBID: | 7X2J |
| Chains: | B_S |
| Organism: | Severe acute respiratory syndrome-related coronavirus, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.40 |
| Reference: | 10.1038/s41467-022-35642-2 |
| Antibody | |
| Antibody: | 70 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >7X2J_B|Chain B|Nb70|Vicugna pacos (30538) QVQLVESGGGLVQAGGSLRLSCVASGRTFSRYAMGWFRQAPGKEREFVAVIEWDGGTSYYVDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAGGNQYYSATYSIWNEYDFWGQGTQVTVSS |
Antigen
Chain: S
Mutation: NULL
| >7X2J_S|Chain A[auth S]|Spike protein S1|Severe acute respiratory syndrome-related coronavirus (694009) RVVPSGDVVRFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVCGPKLS |
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: GLN1 VAL2 THR28 ARG31 TYR32 GLU52 TRP53 ASP54 THR57 GLY100 ASN101 GLN102 TYR103 TYR104 ASN112 GLU113 TYR114 ASP115 PHE116 TRP117 S: LEU355 TYR356 SER358 THR359 PHE361 SER362 THR363 PHE364 LYS365 CYS366 TYR367 GLY368 VAL369 SER370 ALA371 THR372 LYS373 ARG395 ALA398 PRO399 GLY400 GLN401 THR402 ASP414 ASP415 PHE416 MET417 |
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)
