Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6277 |
| PDBID: | 8GPY |
| Chains: | C_B |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.51 |
| Reference: | 10.1038/s41467-023-39267-x |
| Antibody | |
| Antibody: | TH003 scFv |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron BA.4/5 spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Chain: C
Mutation: NULL
| >8GPY_C|Chain C, D[auth E]|scFv|Homo sapiens (9606) EVRLLESGGGLVQPGGSLRLSCAASGFTFNDYAMSWVRQAPGEGLEWVSTISYSGGSTYYADSVKGRFTISRDNSKNMLYLQMNSLRAEDTALYYCANGVATADWYFDLWGRGTLVTVSSQSALTQPRSVSGSPGQSVTISCTGTSSDVGGYNYVSWFQHHPGKAPKLMIYDVTDRPSGVPDRFSGSKSGNTASLTISGLQAEDAADYYCCSYAGTYTVFGGGTKLTVLAAA |
Antigen
Chain: B
Mutation: G7D/S39F/S41P/S43F/T44A/D73N/R76S/K85N/N108K/L120R/S145N/T146K/E152A/F154V/Q166R/N169Y/Y173H
| >8GPY_B|Chain A, B|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSAAA |
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 C: ASP31 TYR32 ALA33 THR50 SER52 TYR53 SER54 SER57 TYR59 THR102 ALA103 ASP104 TRP105 TYR152 TYR154 TYR171 ASP172 ASP175 TYR213 GLY215 B: THR345 ARG346 ASN439 LYS440 LEU441 SER443 LYS444 VAL445 GLY446 GLY447 ASN448 TYR449 ASN450 ARG498 PRO499 THR500 GLN506 |
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)
