Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3438 |
| PDBID: | 7C8W |
| Chains: | A_B |
| Organism: | synthetic construct, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 2.77 |
| Reference: | 10.1038/s41467-021-24905-z |
| Antibody | |
| Antibody: | MR17 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
| >7C8W_A|Chain A|Synthetic nanobody MR17|synthetic construct (32630) QVQLVESGGGLVQAGGSLRLSCAASGFPVEVWRMEWYRQAPGKEREGVAAIESYGHGTRYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNVKDDGQLAYHYDYWGQGTQVTVSAG |
Antigen
Chain: B
Mutation: NULL
| >7C8W_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: GLY26 PHE27 PRO28 VAL31 TRP32 ARG33 GLU35 TYR37 GLY47 VAL48 ALA49 ALA50 GLU52 SER53 TYR54 HIS56 THR58 ARG59 TYR60 ALA61 LYS65 LYS99 ASP101 GLY102 GLN103 LEU104 ALA105 B: ARG403 GLU406 LYS417 GLY446 TYR449 LEU452 TYR453 LEU455 PHE456 ILE472 VAL483 GLU484 GLY485 PHE486 CYS488 TYR489 PHE490 LEU492 GLN493 SER494 TYR495 GLY496 GLN498 ASN501 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)
