Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5669 |
| PDBID: | 7YCN |
| Chains: | CD_B |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 2.85 |
| Reference: | 10.1038/s41467-023-35949-8 |
| Antibody | |
| Antibody: | IY-2A Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | No |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: C
Mutation: NULL
| >7YCN_C|Chain B[auth C], E, H, K|IY-2A Fab heavy chain|Homo sapiens (9606) QVQLVEWGAGLLKPSETLSLTCAVYGGSFSGYYWSWIRQPPGKGLEWIGLINHSGSTNYNPSLKSRVTISLDTSKNQFSLKLTSVTAADTAVYYCARGLGIFGVVTLSDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH |
Light Chain: D
Mutation: NULL
| >7YCN_D|Chain C[auth D], F, I, L|IY-2A Fab light chain|Homo sapiens (9606) ANFMLTQPHSVSESPGKTVTISCTGSSGSIASNYVQWYQQRPGSAPTTVIYEDNQRPSGVPDRFSGSIDSSSNSASLTISGLRTEDEADYYCQSYDSGIWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC |
Antigen
Chain: B
Mutation: NULL
| >7YCN_B|Chain A, D[auth B], G, J|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP |
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)
| C: GLY31 TYR33 LEU50 ASN52 HIS53 SER54 SER56 THR57 ASN58 LEU96 GLY97 ILE98 PHE99 D: ALA29 SER30 ASN31 TYR32 TYR49 GLU50 ASP51 GLN53 SER93 GLY94 B: PHE338 PHE342 ASP364 TYR365 SER366 VAL367 LEU368 TYR369 SER371 ALA372 SER373 PHE374 SER375 THR376 PHE377 LYS378 CYS379 TYR380 SER383 PRO384 THR385 LYS386 LEU387 ASN388 CYS432 ILE434 LEU513 |
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)
