Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5764 |
| PDBID: | 7ZFD |
| Chains: | HL_E |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 3.39 |
| Reference: | 10.1016/j.cell.2022.05.014 |
| Antibody | |
| Antibody: | Omi-25 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron BA.1 spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7ZFD_H|Chain A, D[auth H]|Omi-25 heavy chain|Homo sapiens (9606) QVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQVPGKGLEWVSGISWNSGSIVYADFVKGRFTIARDNAKNSLFLQMNSLRAEDTALYYCAKSTALRHQYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK |
Light Chain: L
Mutation: NULL
| >7ZFD_L|Chain C[auth B], F[auth L]|Omi-25 light chain|Homo sapiens (9606) AIQMTQSPSSLSASVGDRVTITCRTSQTISSYLNWYQQKPGKAPKLLIYDASSLQSGVPSRFSGSGYGTDFTLTISSLQPEDFATYFCQQSYNTPYAFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC |
Antigen
Chain: E
Mutation: G13D/S45L/S47P/S49F/K91N/N114K/G120S/S151N/T152K/E158A/Q167R/G170S/N175Y/Y179H
| >7ZFD_E|Chain B[auth E], E[auth F]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) PNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNHHHHHH |
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)
| H: ALA33 HIS35 TRP47 GLY50 ILE51 SER52 SER57 VAL59 HIS104 GLN105 TYR106 TYR107 TYR108 L: SER30 SER31 TYR32 TYR49 ASP50 SER52 SER53 TYR67 SER91 TYR92 ASN93 THR94 TYR96 E: ARG403 THR415 GLY416 ASN417 ASP420 TYR421 TYR453 LEU455 PHE456 TYR473 ALA475 GLY476 VAL483 ALA484 GLY485 PHE486 ASN487 TYR489 PHE490 ARG493 HIS505 |
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)
