Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5470 |
| PDBID: | 7WTG |
| Chains: | HL_E |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.80 |
| Reference: | 10.1038/s41422-022-00677-z |
| Antibody | |
| Antibody: | XGv051 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7WTG_H|Chain B[auth H]|Heavy chain of XGv051|Homo sapiens (9606) VQLVQSGAEVKKPGSSVKVSCKASGGTFSNYALSWVRQAPGQGLEWMGGIIPIFGTTNYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARLDGYSFGHDRYYQDGMDDWGPGT |
Light Chain: L
Mutation: NULL
| >7WTG_L|Chain C[auth L]|Light chain of XGv051|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTITCRASQAIRNDLGWYQQKPGKAPKCLIYAASSLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYFCLQQNIYPRTFGQGTKV |
Antigen
Chain: E
Mutation: G10D/S42L/S44P/S46F/K88N/N111K/G117S/S148N/T149K/E155A/Q164R/G167S/Q169R/N172Y/Y176H
| >7WTG_E|Chain A[auth E]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) PNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKS |
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: ALA33 GLY50 ILE51 ILE52 PHE55 THR57 THR58 ASN59 TYR102 PHE104 HIS106 ASP107 ARG108 TYR109 TYR110 GLN111 ASP112 L: ARG30 ASN31 ASP32 TYR49 ASN92 ILE93 TYR94 PRO95 E: ARG403 GLY416 ASN417 TYR421 TYR449 LEU452 TYR453 LEU455 PHE456 TYR473 ALA475 GLY476 LYS478 VAL483 ALA484 GLY485 PHE486 ASN487 CYS488 TYR489 PHE490 LEU492 ARG493 SER494 TYR495 SER496 ARG498 TYR501 HIS505 |
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)
