Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5756 |
| PDBID: | 7ZFB |
| Chains: | JK_F |
| Organism: | Lama glama, Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.08 |
| Reference: | 10.1016/j.cell.2022.05.014 |
| Antibody | |
| Antibody: | Omi-18 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; P0DTC2; |
Sequence information
Antibody
Heavy Chain: J
Mutation: NULL
| >7ZFB_J|Chain F[auth H], K[auth J]|Omi-18 heavy chain|Homo sapiens (9606) QVQLVESGGGLIQPGGSLRLSCAASGITVSSNYMTWVRQAPGKGLEWVSLLYAGGSAFYADSVKGRFTISRDNSKNTLYLLMNSLRVGDTAVYYCARDLQVYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK |
Light Chain: K
Mutation: NULL
| >7ZFB_K|Chain G[auth K], J[auth L]|Omi-18 light chain|Homo sapiens (9606) SYELTQPPSVSVAPGQTARITCGGNNDGAKSVHWYQQKPGQAPVLVVYDDSDRPSGIPERFSGSNSGNTATLTITRIEAGDEADYYCQVWDSSRDHVFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS |
Antigen
Chain: F
Mutation: G13D/S45L/S47P/S49F/K91N/N114K/G120S/S151N/T152K/E158A/Q167R/G170S/N175Y/Y179H
| >7ZFB_F|Chain C[auth E], L[auth F]|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: ASN26 GLY28 ALA29 LYS30 ASP49 TRP90 ASP91 SER92 SER93 ARG94 J: GLN1 VAL2 GLY26 ILE27 THR28 SER30 SER31 ASN32 TYR33 TYR52 ALA53 GLY54 SER56 ALA57 PHE58 ARG97 LEU99 GLN100 VAL101 TYR102 ASP105 VAL106 F: ARG403 ASP405 GLU406 ARG408 GLN409 THR415 GLY416 ASN417 ASP420 TYR421 TYR453 LEU455 PHE456 ARG457 LYS458 SER459 ASN460 TYR473 GLN474 ALA475 GLY476 ASN477 LYS478 PHE486 ASN487 TYR489 ARG493 SER496 TYR501 GLY502 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)
