Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4635 |
| PDBID: | 7PRY |
| Chains: | FG_E |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 3.10 |
| Reference: | 10.1016/j.chom.2021.11.013 |
| Antibody | |
| Antibody: | COVOX-45 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Beta variant spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: F
Mutation: NULL
| >7PRY_F|Chain A, F|COVOX-45 Fab heavy chain|Homo sapiens (9606) QVQLVESGGGVVQPGRSLRLSCAASGFTFSTYAMHWVRQAPGKGLEWVAVLSYDGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKGGSYAYYYYMDVWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK |
Light Chain: G
Mutation: NULL
| >7PRY_G|Chain B, G|COVOX-45 Fab light chain|Homo sapiens (9606) DIQLTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGGGSGTDFTFTITSLQPEDIATYYCQQYDNLPLTFGGGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: E
Mutation: K99N/E166K/N183Y
| >7PRY_E|Chain E, J[auth I]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) MGCVAETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGKK |
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)
| F: GLN1 VAL2 GLY26 PHE27 THR31 TYR32 SER52 TYR53 ASP54 SER56 ASN57 TYR59 LYS98 SER101 TYR102 ALA103 TYR104 TYR105 TYR106 TYR107 ASP109 G: SER30 ASN31 TYR32 LEU46 TYR49 ASP50 ASN53 LEU54 GLU55 THR56 TYR91 ASP92 ASN93 E: PRO337 TRP353 ASN354 ARG355 LYS356 ARG357 SER359 ASN360 ASN394 TYR396 PRO426 ASP428 LYS462 PRO463 PHE464 GLU465 ARG466 ILE468 SER514 GLU516 LEU518 HIS519 ALA520 PRO521 THR523 |
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)
