Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5658 |
| PDBID: | 7YAD |
| Chains: | CD_E |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 2.66 |
| Reference: | 10.1038/s41467-022-32665-7 |
| Antibody | |
| Antibody: | S309 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: C
Mutation: NULL
| >7YAD_C|Chain A, D[auth C]|S309 neutralizing antibody heavy chain|Homo sapiens (9606) QVQLVQSGAEVKKPGASVKVSCKASGYPFTSYGISWVRQAPGQGLEWMGWISTYNGNTNYAQKFQGRVTMTTDTSTTTGYMELRRLRSDDTAVYYCARDYTRGAWFGESLIGGFDNWGQGTLVTVS |
Light Chain: D
Mutation: NULL
| >7YAD_D|Chain B, E[auth D]|S309 neutralizing antibody light chain|Homo sapiens (9606) EIVLTQSPGTLSLSPGERATLSCRASQTVSSTSLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQHDTSLTFGGGTKVEIKR |
Antigen
Chain: E
Mutation: G10D/S42L/S44P/S46P/K88N/N111K/G117S/S148N/T149K/E155A/Q164R/G167S/Q169R/N172Y/Y176H
| >7YAD_E|Chain C[auth E], F[auth M]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) PNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKK |
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: PRO28 THR30 SER31 TYR32 TYR54 THR74 TYR100 GLY103 ALA104 TRP105 PHE106 GLU108 SER109 LEU110 ILE111 D: SER30 SER31 THR32 SER33 GLY51 SER53 ASP93 E: THR333 ASN334 LEU335 PRO337 ASP339 GLU340 VAL341 ASN343 ALA344 THR345 ARG346 ASN354 LYS356 ARG357 ILE358 SER359 ASN360 CYS361 LYS440 LEU441 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)
