Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3437 |
| PDBID: | 7C8V |
| Chains: | A_B |
| Organism: | synthetic construct, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 2.15 |
| Reference: | 10.1038/s41467-021-24905-z |
| Antibody | |
| Antibody: | SR4 synthetic-Nanobody |
| 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
| >7C8V_A|Chain A|Synthetic nanobody SR4|synthetic construct (32630) GSSSQVQLVESGGGLVQAGGSLRLSCAASGFPVYSWNMWWYRQAPGKEREWVAAIESHGDSTRYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCYVWVGHTYYGQGTQVTVSAGRAGEQKLISEEDLNSAVDHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >7C8V_B|Chain B|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) AGSPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTGTLEVLFQ |
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: PRO28 TYR30 SER31 TRP32 ASN33 TRP35 TYR37 GLU44 ARG45 TRP47 SER53 HIS54 SER57 ARG59 ALA61 TYR97 TRP99 VAL100 GLY101 THR103 TYR105 B: VAL445 GLY446 TYR449 LEU452 TYR453 LEU455 PHE456 GLU484 GLY485 TYR489 PHE490 LEU492 GLN493 SER494 TYR495 GLY496 GLN498 THR500 ASN501 GLY502 TYR505 |
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)
