Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5748 |
| PDBID: | 7ZFA |
| Chains: | JK_C |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 4.24 |
| Reference: | 10.1016/j.cell.2022.05.014 |
| Antibody | |
| Antibody: | Omi-6 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron BA.1 spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: J
Mutation: NULL
| >7ZFA_J|Chain E, H, S[auth J], T[auth M]|Omi-6 heavy chain|Homo sapiens (9606) EVQLLESGPGLVKPSETLSLTCTVSGGSISRYSWSWIRQPAGRGLEWIGRMYSSGGTNYNPSLESRVTMSLDTSKKQFSLKLSSVTAADTAVYYCAAASIDQVWGTYRDAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK |
Light Chain: K
Mutation: NULL
| >7ZFA_K|Chain F, G[auth K], I[auth L], J[auth N]|Omi-6 light chain|Homo sapiens (9606) AIRMTQSPSSLAASVGDRVTISCRAGQSISSFLHWYQQKVGKAPKLLIYDASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFAAYYCQQSYENPLTFGGGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: C
Mutation: G13D/S45L/S47P/S49F/K91N/N114K/G120S/S151N/T152K/E158A/Q167R/G170S/N175Y/Y179H
| >7ZFA_C|Chain A, B, C, D|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) HHHHHHTNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGKK |
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)
| K: SER30 SER31 PHE32 HIS34 ASP50 SER91 TYR92 GLU93 ASN94 LEU96 J: SER28 SER30 ARG31 SER33 ARG50 TYR52 SER53 SER54 GLY56 THR57 ASN58 TYR59 THR73 LYS76 ASP101 GLN102 VAL103 TRP104 GLY105 THR106 TYR107 ARG108 ASP109 C: THR345 ARG346 PHE347 ALA348 SER349 TYR351 ALA352 ASN354 LEU441 LYS444 SER446 GLY447 ASN448 TYR449 ASN450 LEU452 ILE468 THR470 ILE472 GLY482 VAL483 ALA484 PHE490 LEU492 ARG493 SER494 SER496 ARG498 |
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)
