Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5291 |
| PDBID: | 7VOA |
| Chains: | A_B |
| Organism: | Vicugna pacos, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 1.80 |
| Reference: | 10.1038/s41422-022-00700-3 |
| Antibody | |
| Antibody: | aRBD-2-5 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: A
Mutation: NULL
| >7VOA_A|Chain A|alpaca nanobody|Vicugna pacos (30538) QVQLVESGGGLVQPGGTLRLSCAASGFTLDYYAIGWFRQAPGKEREGVSCISGSGGITNYTDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAPVSHTVVAGCAFEAWTDFGSWGQGTQVTVSS |
Antigen
Chain: B
Mutation: NULL
| >7VOA_B|Chain B|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK |
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: VAL2 PHE27 TYR31 TYR32 SER52 GLY53 SER54 GLY56 ILE57 THR58 PRO98 VAL99 SER100 HIS101 THR102 VAL103 VAL104 ALA105 TRP112 THR113 ASP114 PHE115 B: GLY446 GLY447 ASN448 TYR449 LEU452 TYR453 LEU455 PHE456 THR470 VAL483 GLU484 GLY485 PHE486 ASN487 TYR489 PHE490 LEU492 GLN493 SER494 TYR495 GLY496 |
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)
