Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3767 |
| PDBID: | 7FH0 |
| Chains: | C_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 3.20 |
| Reference: | 10.1038/s41422-022-00700-3 |
| Antibody | |
| Antibody: | aRBD-2-7 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2; P0DTC2; P0DTC2; P0DTC2; |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >7FH0_C|Chain B, C|nanobodies aRBD-2-7|Vicugna pacos (30538) QVQLVESGGGLVQAGGSLRLSCAASGRTYTMGWFRQAPGKEREFVAAMRWSDTDYADSLKGRFTISRDNANNAMYLQMNSLGPEDTAVYYCAAGEAWLARSTHHYDYWGQGTQVTVSSGGGGSGGGGSGGGGSQLQLVESGGGLVQAGGSLRLSCAASERTFSGGVMGWFRQRPGKEREFVAAIRWNGASTFYADSVKGRFTCSRDNAKNTGYLQMNSLTPEDTAVYYCARAVRTYASSDYYFQERTYDYWGQGTQVTVSS |
Antigen
Chain: A
Mutation: NULL
| >7FH0_A|Chain A|Spike protein S1,Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNK |
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: ARG27 TYR29 ARG49 TRP50 ASP52 ASP57 GLU95 ALA96 TRP97 LEU98 ARG100 SER101 HIS103 HIS104 THR161 PHE162 SER163 GLY164 ARG185 ASN187 GLY188 ALA189 SER190 THR191 PHE192 TYR193 LYS198 VAL233 ARG234 THR235 TYR236 ALA237 SER238 SER239 A: TYR351 LYS444 TYR449 ASN450 LEU452 LEU455 PHE456 THR470 ILE472 GLY482 VAL483 GLU484 GLY485 TYR489 PHE490 LEU492 GLN493 SER494 GLY496 GLY632 THR634 GLY635 LYS636 ASP639 TYR640 LEU674 PHE675 ARG676 LYS677 SER678 ASN679 TYR692 GLN693 ALA694 GLY695 SER696 PRO698 PHE705 ASN706 TYR708 |
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)
