Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5475 |
| PDBID: | 7WTJ |
| Chains: | HL_E |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 4.20 |
| Reference: | 10.1038/s41422-022-00677-z |
| Antibody | |
| Antibody: | XGv286 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
| >7WTJ_H|Chain A[auth H]|Heavy chain of XGv286|Homo sapiens (9606) VQLVQSGAEVKKPGASVKVSCKASGYTFSSYYIHWVRQAPGQGPEWMAIINPGDGGASYAQKFQGRVTLTRDTSTSTLYMELSSLRSEDTAVYYCARAEGSSWLGWFDPWGQGTLVTV |
Light Chain: L
Mutation: NULL
| >7WTJ_L|Chain B[auth L]|Light chain of XGv286|Homo sapiens (9606) SVLTQPPSASGTPGQRVTISCSGSSSNIGSNYVYWYQQLPGTAPKLLIYRNNQRPSGVPDRFSGSRSGTSASLAISGLRSEDEADYYCAAWDDGLSGSGWVFGGGTKLT |
Antigen
Chain: E
Mutation: G10D/S42L/S44P/S46F/K88N/N111K/G117S/S148N/T149K/E155A/Q164R/G167S/Q169R/N172Y/Y176H
| >7WTJ_E|Chain C[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)
| Chain residues position delta_SASA
: residuesposition H: TYR33 TRP47 ILE50 ASN52 ASP55 GLY57 ALA58 SER59 TYR60 ALA61 GLN65 TRP104 LEU105 L: ASN32 TRP92 ASP94 GLY95 LEU96 SER97 GLY98 SER99 E: ASN437 ASN439 LYS440 SER443 LYS444 VAL445 SER446 ARG498 PRO499 THR500 TYR501 GLY502 VAL503 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)
