Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 4765 |
| PDBID: | 7RKS |
| Chains: | IM_S |
| Organism: | Homo sapiens, Severe acute respiratory syndrome-related coronavirus |
| Method: | XRD |
| Resolution (Å): | 2.70 |
| Reference: | 10.1016/j.celrep.2021.109760 |
| Antibody | |
| Antibody: | C118 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | |
Sequence information
Antibody
Heavy Chain: I
Mutation: NULL
| >7RKS_I|Chain A[auth H], B[auth I]|C118 Antibody Fab Heavy Chain|Homo sapiens (9606) QVQLVESGGGVVQPGRSLRLSCAASGFTFSNYAMHWVRQAPGKGLEWVAVISYDGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAIYYCASGYTGYDYFVRGDYYGLDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKHHHHHH |
Light Chain: M
Mutation: NULL
| >7RKS_M|Chain C[auth L], D[auth M]|C118 Antibody Fab Light Chain|Homo sapiens (9606) QPVLTQSPSASASLGASVKLTCTLSSGHSSYAIAWHQQQPEKGPRYLMKLNTDGSHSKGDGIPDRFSGSSSGAERYLTISSLQSEDEADYYCQTWGTGILVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT |
Antigen
Chain: S
Mutation: NULL
| >7RKS_S|Chain E[auth R], F[auth S]|Spike protein S1|Severe acute respiratory syndrome coronavirus (694009) NLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTFFSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCVLAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLNDYGFYTTTGIGYQPYRVVVLSFELLNAPATVHHHHHH |
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)
| I: GLY26 PHE27 THR28 ASN31 TYR32 TYR52 SER55 ASN56 TYR96 THR97 GLY98 TYR99 M: LYS49 ASN51 ASP53 LYS54 GLY55 ASP56 ASP60 S: LEU355 TYR356 SER358 THR359 PHE361 SER362 PHE364 LYS365 CYS366 TYR367 GLY368 VAL369 SER370 ALA371 THR372 LYS373 GLY391 ASP392 ARG395 PRO399 GLY400 GLN401 THR402 ASP414 ASP415 PHE416 MET417 ASN424 ILE489 GLY490 TYR491 TYR494 |
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)
