Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6391 |
| PDBID: | 8HR2 |
| Chains: | B_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Vicugna pacos |
| Method: | XRD |
| Resolution (Å): | 1.94 |
| Reference: | 10.1016/j.jsb.2023.107996 |
| Antibody | |
| Antibody: | 1C6 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >8HR2_B|Chain B|NB1C6|Vicugna pacos (30538) QVQLQESGGGSVQAGGRLRLSCAASGDTYSSYCMGWFRQAPGKEREGVAAIYIGGDNTYYADSAKGRFTISQDYDKNTAYLQMNSLKSEDTAMYYCAAELFCPWPDIGTMSPAEYKYWGQGTQVTVSS |
Antigen
Chain: A
Mutation: NULL
| >8HR2_A|Chain A|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATSRAAADYKDDDDK |
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: ASP27 TYR29 SER30 SER31 TYR52 GLY54 GLY55 TYR74 GLU99 LEU100 PHE101 CYS102 PRO103 TRP104 PRO105 ASP106 THR109 MET110 GLU114 LYS116 A: ALA352 TRP353 ASN354 ARG355 LYS356 ARG357 TYR396 ARG457 LYS462 PRO463 PHE464 GLU465 ARG466 ASP467 ILE468 SER469 GLU516 LEU517 |
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)
