Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5630 |
| PDBID: | 7XSB |
| Chains: | JK_C |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | XRD |
| Resolution (Å): | 3.20 |
| Reference: | 10.1038/s41590-023-01449-6 |
| Antibody | |
| Antibody: | P5S-3B11 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: J
Mutation: NULL
| >7XSB_J|Chain E[auth D], G, I[auth H], K[auth J]|P5S-3B11 Heavy chain|Homo sapiens (9606) EVQLVESGGGLVQPGGSLRISCAASGLTFTGYWMNWVRQAPGKGLEWVANIKEDGSEKYYVDSVKGRFTISRDNAKNSLYLQMNSLRVEDTAVYYCARLRWLRGNFDHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKV |
Light Chain: K
Mutation: NULL
| >7XSB_K|Chain F, H[auth I], J[auth K], L|P5S-3B11 Light chain|Homo sapiens (9606) NFMLTQPHSVSESPGKTVTISCTGSNGYIANNYVQWYQQRPGSVPTVVIYEDNQRPSGVPDRFSGSIDSSSNSASLIISGLKTEDEADYYCQSYDTPNVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS |
Antigen
Chain: C
Mutation: K126N/E193K/N210Y
| >7XSB_C|Chain A, B, C, D[auth E]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAADPTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKHHHHHH |
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)
| J: GLY31 TYR32 TRP33 LYS52 GLU53 GLU57 TYR59 ARG100 TRP101 LEU102 ARG103 K: TYR28 ALA30 ASN31 ASN32 TYR33 TYR50 GLU51 ASP52 GLN54 ILE67 SER69 SER70 TYR94 THR96 PRO97 C: SER366 TYR369 ASN370 SER371 ALA372 SER373 PHE374 SER375 THR376 PHE377 LYS378 CYS379 TYR380 SER383 PRO384 THR385 LYS386 GLY404 ASP405 VAL407 ARG408 GLN414 |
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)
