Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3099 |
| PDBID: | 6WAQ |
| Chains: | C_D |
| Organism: | Lama glama, Severe acute respiratory syndrome-related coronavirus |
| Method: | XRD |
| Resolution (Å): | 2.20 |
| Reference: | 10.1016/j.cell.2020.04.031 |
| Antibody | |
| Antibody: | SARS 72 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >6WAQ_C|Chain A, C|nanobody SARS VHH-72|Lama glama (9844) QVQLQESGGGLVQAGGSLRLSCAASGRTFSEYAMGWFRQAPGKEREFVATISWSGGSTYYTDSVKGRFTISRDNAKNTVYLQMNSLKPDDTAVYYCAAAGLGTVVSEWDYDYDYWGQGTQVTVSSGS |
Antigen
Chain: D
Mutation: NULL
| >6WAQ_D|Chain B, D|Spike glycoprotein|Human SARS coronavirus (694009) TNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFEGSLEVLFQ |
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)
| C: GLU31 GLU46 PHE47 TRP52 SER53 GLY55 SER56 THR57 TYR58 TYR59 THR60 ASP61 GLY98 THR99 D: LEU355 TYR356 ASN357 SER358 THR359 PHE360 PHE361 SER362 THR363 PHE364 LYS365 CYS366 ALA371 THR372 GLY391 ASP392 VAL394 ARG395 TRP423 ASN424 ARG426 ASN427 ILE489 GLY490 TYR494 |
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)
