Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4524 |
| PDBID: | 7ORB |
| Chains: | AB_R |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.50 |
| Reference: | 10.1016/j.cell.2021.06.020 |
| Antibody | |
| Antibody: | COVOX-75 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: A
Mutation: NULL
| >7ORB_A|Chain D[auth A], I[auth E]|COVOX-75 Fab heavy chain|Homo sapiens (9606) QVQLVESGGGVVQPGRSLRLSCAASGFTFNNYPLHWVRQAPGKGPEWVAVISQDGGNKYYVDSVKGRFTISRDNSKNTLYLQMNNLRAEDTALYYCARDVVVVVAARNHYYNGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK |
Light Chain: B
Mutation: NULL
| >7ORB_B|Chain E[auth B], J[auth F]|COVOX-75 Fab light chain|Homo sapiens (9606) DIQLTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLIYAVSSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQAKSFPFTFGPGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: R
Mutation: L129R
| >7ORB_R|Chain A[auth R], F[auth X]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) ETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGKK |
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)
| A: TYR59 VAL102 VAL104 ALA105 ALA106 ARG107 HIS109 TYR110 TYR111 ASN112 B: SER30 SER31 TRP32 ALA50 SER67 GLY68 ALA91 LYS92 SER93 PHE94 PHE96 R: THR345 ARG346 ASN440 LEU441 ASP442 SER443 LYS444 VAL445 GLY446 GLY447 ASN448 TYR449 ASN450 ARG452 GLU484 PHE490 LEU492 GLN493 SER494 TYR495 GLY496 GLN498 PRO499 THR500 |
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)
