Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6417 |
| PDBID: | 8J5J |
| Chains: | E_A |
| Organism: | Betacoronavirus sp., Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 3.00 |
| Reference: | 10.24272/j.issn.2095-8137.2023.187 |
| Antibody | |
| Antibody: | S43 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | Bat coronavirus RsYN04 RBD-S43 |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Chain: E
Mutation: NULL
| >8J5J_E|Chain B[auth E]|nano antibody S43|Vicugna pacos (30538) MHSSALLCCLVLLTGVRAQVQLQESGGGLVQPGGSLRLTCAPSGFTLDYYAIGWFRQAPGKEREGVSCISSNNSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAAEPDYSGVYYYTCGWTDFGSWGQGTQVTVSS |
Antigen
Chain: A
Mutation: NULL
| >8J5J_A|Chain A|Spike protein S1|Betacoronavirus sp. (1928434) RVTPSQSVARYPNITNLCPFSQVFNATRFPSVYAWTRERISNCIADYSVLYNSTSFSTFRCYGVSPTKLNDLCFSNVYADSMVVRGDEVRQIAPSQTGVIADYNYKLPDDFTGCVIAWNSKAKDENGQYFYRLFRKSKLLPFQRDVSNVTYGSGKNDGCNPSEADCYWPLLKYGFTSSVSQDYQPYRVVVLSFELLNAPATVCGPKRSTELVYNKCVNF |
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)
| E: GLU62 ARG63 GLU116 PRO117 ASP118 TYR119 SER120 GLY121 VAL122 TYR123 TYR124 TYR125 THR126 GLY128 TRP129 THR130 ASP131 PHE132 GLY133 A: TYR51 ASN52 PHE56 SER57 THR58 PHE59 ARG60 CYS61 TYR62 GLY63 VAL64 SER65 PRO66 GLY86 ASP87 VAL89 ARG90 PRO94 SER95 GLN96 ASP109 PHE111 GLN181 ASP182 TYR186 |
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)
