Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6392 |
| PDBID: | 8HR2 |
| Chains: | C_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: | 1B5 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: C
Mutation: NULL
| >8HR2_C|Chain C|NB1B5|Vicugna pacos (30538) QVQLQESGGGSVQAGGSLRLSCAASGYTYSTYCMGWFRQAPGKEREGVATIDSDGRTRYADSVKGRFTISEDNAKNTLYLQMNSLKPEDTAMYYCAADSGWVGYSLDPYQYNYWGQGTQVTVSS |
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)
| C: GLU44 ASP54 ARG56 THR57 ARG58 ASP61 SER99 GLY100 TRP101 VAL102 GLY103 TYR104 SER105 LEU106 ASP107 TYR109 GLN110 A: TYR365 TYR369 ASN370 SER371 ALA372 PHE374 SER375 THR376 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 GLY404 VAL407 ARG408 VAL503 |
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)
