Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6077 |
| PDBID: | 8DXU |
| Chains: | AB_R |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.73 |
| Reference: | 10.1038/s41467-023-36295-5 |
| Antibody | |
| Antibody: | GAR03 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: A
Mutation: NULL
| >8DXU_A|Chain D[auth A]|Heavy chain of Fab arm of antibody GAR03|Homo sapiens (9606) QVQLVQSGAEVKKPGASVKVSCKASGYTFSSYDINWVRQAPGQGLEWMGWMSPNSGNTGYAQKFQGRVTMTRSTSMSTAYMELSSLRSEDTAVYFCARMSSSLTNYLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH |
Light Chain: B
Mutation: NULL
| >8DXU_B|Chain E[auth B]|Light chain of Fab arm of antibody GAR03|Homo sapiens (9606) SYVLTQPPSVAVAPGQTARIRCGENDIGSKNVHWYQQKSGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSTGDHPDVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC |
Antigen
Chain: R
Mutation: NULL
| >8DXU_R|Chain A[auth R]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKGSHHHHHH |
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: TRP50 SER55 ASN57 THR58 SER102 LEU103 THR104 ASN105 B: SER1 TYR2 ASP26 GLY28 SER29 LYS30 ASN31 TYR48 ASP49 ASP50 SER51 ASP52 ASN65 GLY67 ASN68 TRP90 SER92 THR93 GLY94 ASP95 HIS96 PRO97 R: PRO337 GLU340 VAL341 ALA344 THR345 ARG346 PHE347 ALA348 SER349 TYR351 ALA352 TRP353 ASN354 ARG355 LYS356 ARG357 SER359 ASN360 TYR396 ASN450 LYS458 PHE464 ARG466 ILE468 SER469 THR470 GLU471 |
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)
