Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5328 |
| PDBID: | 7WEF |
| Chains: | CL_E |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 3.80 |
| Reference: | 10.1038/s41586-022-04466-x |
| Antibody | |
| Antibody: | XGv289 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron variant spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: C
Mutation: NULL
| >7WEF_C|Chain A[auth C]|The heavy chain of Fab XGv289|Homo sapiens (9606) QVQLVQSGAEVKKPGASLKVSCRASGYTFTSHFIHWVRQAPGQGLEWMGIINPSGGASYAQNFRDRVTMTTDPSTSTVYMELGSLRSEDTAVYYCARAEGSSWLGWFDPWGQGTLVTVSS |
Light Chain: L
Mutation: NULL
| >7WEF_L|Chain C[auth L]|The light chain of Fab XGv289|Homo sapiens (9606) SVLTQPPSASGTPGQRVTIPCSGSSSNIGNNYVYWYQQLPGTAPKLLVYGNNQRPSGVPDRFSVSKSGTSASLAISGLRSEDEADYYCAAWDDGLSGSGWVFGGGTKLTVL |
Antigen
Chain: E
Mutation: G10D/S42L/S44P/S46F/S148N/T149K/E155A/Q164R/G167S/Q169R/N172Y/Y176H
| >7WEF_E|Chain B[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)
| C: PHE33 TRP47 ILE50 ASN52 GLY56 ALA57 SER58 TYR59 ALA60 GLN61 ARG64 TRP103 L: ASN31 ASN32 TRP92 ASP94 GLY95 LEU96 SER97 GLY98 SER99 E: PHE374 ASN437 ASN439 ASN440 SER443 LYS444 VAL445 GLY446 ARG498 PRO499 THR500 TYR501 GLY502 VAL503 GLN506 |
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)
