Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3562 |
| PDBID: | 7D2Z |
| Chains: | A_B |
| Organism: | synthetic construct, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 1.97 |
| Reference: | 10.1371/journal.ppat.1009328 |
| Antibody | |
| Antibody: | SR31 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
| >7D2Z_A|Chain A|SR31 against SARS-CoV-2 RBD, non neutralizing|synthetic construct (32630) GSSSQVQLVESGGGLVQAGGSLRLSCAASGFPVWQGEMAWYRQAPGKEREWVAAISSMGYKTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAVMVGFWYAGQGTQVTVSAGRAGEQKLISEEDLNSAVDHHHHHH |
Antigen
Chain: B
Mutation: NULL
| >7D2Z_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: SER-2 SER-1 SER0 GLN1 VAL2 GLN3 LEU4 GLY26 PHE27 PRO28 GLN31 GLY32 GLU33 ALA35 TYR37 ARG45 TRP47 VAL48 ALA49 ALA50 ILE51 SER52 SER53 MET54 GLY55 TYR59 TYR60 ALA61 TYR95 MET99 VAL100 GLY101 PHE102 TRP103 TYR104 ALA105 GLY106 GLN107 B: PHE338 PHE342 ALA363 ASP364 TYR365 SER366 VAL367 LEU368 TYR369 ASN370 SER371 PHE374 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 LYS386 LEU387 ASN388 ILE434 LEU513 LYS528 LYS529 SER530 GLY532 THR533 LEU534 GLU535 LEU537 PHE538 |
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)
