Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3730 |
| PDBID: | 7F5H |
| Chains: | C_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 3.00 |
| Reference: | 10.3389/fmicb.2022.875840 |
| Antibody | |
| Antibody: | DL28 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >7F5H_C|Chain C, D|Nanobody DL28|Vicugna pacos (30538) GSSSQVQLQESGGGLVQAGGSLRLSCAASGSDFSSSTMGWYRQAPGKQREFVAISSEGSTSYAGSVKGRFTISRDNAKNTVYLQMNSLEPEDTAVYYCNVVDRWYDYWGQGTQVTVSAGRAGEQKLISEEDLNSAVDHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >7F5H_A|Chain A, B|SARS-CoV-2 Spike Receptor-Binding Domain (RBD)|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)
| C: GLN1 SER31 SER32 THR33 TYR37 GLN39 LYS43 GLN44 ARG45 PHE47 ILE50 SER52 GLY54 SER55 THR56 SER57 TYR58 ALA59 GLY60 LYS63 ASN95 VAL97 ASP98 ARG99 TRP100 TYR101 ASP102 TYR103 TRP104 A: ALA344 THR345 ARG346 PHE347 ALA348 SER349 TYR351 ALA352 TRP353 ASN354 ARG355 LYS356 LYS444 GLY446 TYR449 ASN450 TYR451 LEU452 ARG466 ILE468 SER469 THR470 GLU471 ILE472 ASN481 GLY482 VAL483 GLU484 PHE490 LEU492 GLN493 SER494 |
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)
