Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4847 |
| PDBID: | 7S83 |
| Chains: | A_C |
| Organism: | Ginglymostoma cirratum, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 2.52 |
| Reference: | 10.1038/s41467-023-36106-x |
| Antibody | |
| Antibody: | ShAb01 variable new antigen receptor (VNAR) 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: A
Mutation: NULL
| >7S83_A|Chain C[auth A]|ShAb01 VNAR|Ginglymostoma cirratum (7801) ARVDQTPRSVTKETGESLTINCVLRDSNCALSSTHWYRKKSGSTNEERILQGRRYVETVNSGSKSFSLRINDLRVEDSGTYRCKVYWGNSWQDKFCPGLGSYEYGDGTAVTVNGPLEVLFQGPHHHHHHHH |
Antigen
Chain: C
Mutation: NULL
| >7S83_C|Chain B[auth C]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) NITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPGSHHHHHH |
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)
| A: ALA1 ARG2 ARG8 GLU46 ARG82 LYS84 TYR86 TRP87 LYS94 PHE95 CYS96 PRO97 GLY98 LEU99 GLY100 SER101 TYR102 GLU103 TYR104 ASP106 C: TYR369 SER371 ALA372 PHE374 SER375 THR376 PHE377 LYS378 CYS379 TYR380 GLY381 VAL382 SER383 PRO384 THR385 LYS386 ARG408 ALA411 PRO412 GLY413 GLN414 ASP427 ASP428 PHE429 GLY502 VAL503 TYR508 |
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)
