Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5300 |
| PDBID: | 7W1S |
| Chains: | B_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 2.00 |
| Reference: | 10.3389/fimmu.2022.820336 |
| Antibody | |
| Antibody: | Nb-007 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: B
Mutation: NULL
| >7W1S_B|Chain B|Nanobody Nb-007|Vicugna pacos (30538) QLQLVESGGGLVQAGGSMRLSCAASISFSSFPMGWHRQAPGKQRELVAKTGIGGTAYDDSVKGRFTISRDNTKNTVYLQMNSLKVEDTAVYYCWGWRMNDYWGQGTQVTVSSHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >7W1S_A|Chain A|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) VQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNK |
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: SER25 ILE26 SER27 SER29 SER30 PHE31 PRO32 LYS49 GLY51 ILE52 GLY53 GLY54 THR55 ALA56 TRP96 ARG97 MET98 A: TYR351 VAL445 GLY446 GLY447 TYR449 ASN450 LEU452 THR470 VAL483 GLU484 PHE490 LEU492 GLN493 SER494 TYR495 GLY496 GLN498 |
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)
