Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5326 |
| PDBID: | 7WED |
| Chains: | HL_E |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.50 |
| Reference: | 10.1038/s41586-022-04466-x |
| Antibody | |
| Antibody: | XGv347 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron variant spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7WED_H|Chain B[auth H]|The heavy chain of Fab XGv347|Homo sapiens (9606) QMQLVQSGPEVKKPGTSVKVSCKASGFTFTDVSSLQWVRQARGQRLEWIGWTVVGTGNTNYAPRFQERVTITTDKSTSTAYMELSSLRSEDTAVYYCAAPFCSETSCSDGFDLWGQGTKVTVS |
Light Chain: L
Mutation: NULL
| >7WED_L|Chain C[auth L]|The light chain of Fab XGv347|Homo sapiens (9606) EIVLTQSPGTLSLSPGDRATLSCRASQSVRISYLAWYQQKPGQAPRLLISGSSSRATGIPDRFSASGSGTDFTLTISRLEPEDFAVYYCQQYANSPWTFGQGTKVEV |
Antigen
Chain: E
Mutation: G10D/S42L/S44P/S46F/S148N/T149K/E155A/Q164R/G167S/Q169R/N172Y/Y176H
| >7WED_E|Chain A[auth E]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) PNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKS |
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)
| H: ASP31 VAL32 SER34 TRP51 VAL53 GLY55 THR56 PRO100 GLU104 THR105 SER106 CYS107 SER108 ASP109 GLY110 PHE111 L: ARG30 SER32 TYR33 GLY51 SER53 SER54 TYR92 TRP97 E: TYR421 LEU455 PHE456 TYR473 ALA475 GLY476 ASN477 LYS478 PRO479 CYS480 ASN481 GLY485 PHE486 ASN487 CYS488 TYR489 PHE490 ARG493 |
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)
