Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 3766 |
| PDBID: | 7FH0 |
| Chains: | B_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: B
Mutation: NULL
| >7FH0_B|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)
| B: 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: GLY413 THR415 GLY416 LYS417 ASP420 TYR421 LYS424 ASP427 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 LYS462 TYR473 GLN474 ALA475 GLY476 SER477 PRO479 PHE486 ASN487 TYR489 LYS663 TYR668 ASN669 LEU671 LEU674 PHE675 THR689 ILE691 GLY701 VAL702 GLU703 GLY704 TYR708 PHE709 LEU711 GLN712 SER713 GLY715 |
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)
