Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6428 |
| PDBID: | 8SK5 |
| Chains: | B_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Lama glama |
| Method: | XRD |
| Resolution (Å): | 2.01 |
| Reference: | 10.1038/s41598-023-40919-7 |
| Antibody | |
| Antibody: | 7A9 VHH |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: B
Mutation: NULL
| >8SK5_B|Chain B|anti-SARS-CoV-2 receptor binding domain VHH|Lama glama (9844) QVQLVESGGGLVQAGGSLRLSCSASGGTASRSAMGWFRQAPGKEREFVAGISRRNSGSTYVADSYEDSVKGRFTISRDNAKNTIYLQMNSLKPEDTAVYYCAAEPTLGWYVPRRSVEYEYWGQGTQVTVSSAAADYKDHDGDYKDHDIDYKDDDDKGAAHHHHHH |
Antigen
Chain: A
Mutation: NULL
| >8SK5_A|Chain A|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFSGHHHHHH |
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)
| Chain residues position delta_SASA
: residuesposition B: GLN1 ARG31 ARG53 SER58 TYR60 ALA62 SER64 GLU104 PRO105 THR106 LEU107 GLY108 TRP109 TYR110 VAL111 ARG113 ARG114 GLU117 GLU119 A: TRP353 ASN354 ARG355 ARG357 SER359 ASN360 THR393 ASN394 TYR396 ARG457 LYS462 PRO463 PHE464 GLU465 ARG466 ILE468 SER514 GLU516 LEU518 ALA520 PRO521 THR523 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
