Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6315 |
| PDBID: | 8GZ5 |
| Chains: | B_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 1.70 |
| Reference: | 10.1093/jb/mvac096 |
| Antibody | |
| Antibody: | P17 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Alpha spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >8GZ5_B|Chain B|Nanobody P17|Vicugna pacos (30538) QVQLQESGGGLVQAGGSLRLSCAASGRTSSVYNMAWFRQTPGKEREFVAAITGNGGTTLYADSVKGRLTISRGNAKNTVSLQMNVLKPDDTAVYYCAAGGWGKERNYAYWGQGTQVTVSSHHHHHH |
Antigen
Chain: A
Mutation: N169Y
| >8GZ5_A|Chain A|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSHHHHHHHH |
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: SER29 SER30 VAL31 TYR32 ASN33 GLN39 GLU44 ARG45 THR52 GLY53 ASN54 GLY99 GLY100 TRP101 ARG105 ASN106 TYR107 ALA108 TYR109 TRP110 A: VAL445 GLY446 TYR449 LEU452 TYR453 THR470 GLU471 ILE472 GLY482 VAL483 GLU484 GLY485 PHE486 TYR489 PHE490 LEU492 GLN493 SER494 GLY496 GLN498 TYR501 |
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)
