Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4519 |
| PDBID: | 7OR9 |
| Chains: | HL_E |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.34 |
| Reference: | 10.1016/j.cell.2021.06.020 |
| Antibody | |
| Antibody: | COVOX-278 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7OR9_H|Chain D[auth H]|COVOX-278 Fab heavy chain|Homo sapiens (9606) QVQLVQSGAEVKKPGASVKVSCKASGYIFIRYGISWVRQAPGQGLEWMGWISANNGYTNYAQKLQGRVTMTTDTSTSTAYMELRSLRSDDTAVYYCARDGGILTGYLDYFDHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK |
Light Chain: L
Mutation: NULL
| >7OR9_L|Chain E[auth L]|COVOX-278 Fab light chain|Homo sapiens (9606) DIQMTQSPSSLSASVGDRLTITCRASQSIASYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYHCQQSYSTLGITFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: E
Mutation: NULL
| >7OR9_E|Chain A[auth E]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) ETGHHHHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGKK |
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: ILE30 ARG31 TRP50 ASN54 TYR57 ASN59 ILE102 LEU103 THR104 GLY105 TYR106 LEU107 ASP108 L: ILE2 GLN27 SER28 ALA30 SER31 TYR32 TYR49 ALA50 SER52 SER91 TYR92 SER93 THR94 LEU95 E: THR345 ARG346 SER349 TYR351 ASN440 LEU441 ASP442 SER443 LYS444 VAL445 GLY446 GLY447 ASN448 TYR449 ASN450 TYR451 LEU452 THR470 GLU484 PHE490 LEU492 PRO499 |
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)
