Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 7206 |
| PDBID: | 7MDW |
| Chains: | B_R |
| Organism: | Lama glama, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 3.58 |
| Reference: | 10.1038/s41467-021-24963-3 |
| Antibody | |
| Antibody: | 105 Nanobody |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >7MDW_B|Chain C[auth B]|nanobody Nb105|Lama glama (9844) VQLVESGGGLVQAGGSLRLSCAVSGRTFSTYGMAWFRQAPGKERDFVATITRSGETTLYADSVKGRFTISRDNAKNTVYLQMNSLKIEDTAVYYCAVRRDSSWGYSRDLFEYDYWGQGTQVTVS |
Antigen
Chain: R
Mutation: NULL
| >7MDW_R|Chain B[auth R]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG |
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: GLU44 THR57 LEU59 ARG99 ARG100 SER102 SER103 TRP104 GLY105 TYR106 SER107 ARG108 ASP109 LEU110 PHE111 GLU112 R: TYR369 ASN370 ALA372 PHE374 SER375 THR376 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 GLY404 ASP405 VAL407 ARG408 VAL503 TYR508 |
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)
