Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5471 |
| PDBID: | 7WTH |
| Chains: | HL_E |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 4.30 |
| Reference: | 10.1038/s41422-022-00677-z |
| Antibody | |
| Antibody: | XGv264 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
| >7WTH_H|Chain C[auth H]|Heavy chain of XGv264|Homo sapiens (9606) ITLKESGPTLVKPTQTLTLTCAFSGFSLNTGGAGVGWIRQPPGKALEWLALIYWDGDKRYNPSLKSRLAIIMDTSKNRVVLTMTNMDPVDTATYYCAHHKIEYIFDYWGQGTLVAVSS |
Light Chain: L
Mutation: NULL
| >7WTH_L|Chain B[auth L]|Light chain of XGv264|Homo sapiens (9606) ALTQPASVSGSPGQSITVSCTGTSSDLGNFQYVSWYQHHPGKAPKLLIYEVSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCCSYTTTTIPVAFGGGTRL |
Antigen
Chain: E
Mutation: G10D/S42L/S44P/S46F/K88N/N111K/G117S/S148N/T149K/E155A/Q164R/G167S/Q169R/N172Y/Y176H
| >7WTH_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)
| L: GLY30 ASN31 PHE32 GLN33 TYR34 GLU52 TYR93 THR94 THR95 PRO99 VAL100 H: ASN30 THR31 GLY32 GLY33 TRP49 LEU52 TYR54 ASP56 ASP58 ARG60 HIS100 LYS101 ILE102 GLU103 E: THR345 ARG346 ASN437 ASN439 LYS440 LEU441 ASP442 SER443 LYS444 VAL445 SER446 GLY447 TYR449 ASN450 ARG498 PRO499 THR500 TYR501 GLY502 VAL503 GLN506 ARG509 |
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)
