Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 6432 |
| PDBID: | 8SMT |
| Chains: | HL_E |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | XRD |
| Resolution (Å): | 3.16 |
| Reference: | 10.1016/j.str.2023.11.015 |
| Antibody | |
| Antibody: | WRAIR-2134 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: H
Mutation: NULL
| >8SMT_H|Chain A, C[auth D], E[auth H], F[auth I]|WRAIR-2134 Fab heavy chain|Homo sapiens (9606) EVQLVESGGGVVQPGRSLRLSCAASGFIFSSYGMYWVRQAPGKGLEWVAVIWYDGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDLSSSSGWDDYYYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC |
Light Chain: L
Mutation: NULL
| >8SMT_L|Chain B, D[auth F], G[auth J], H[auth L]|WRAIR-2134 Fab light chain|Homo sapiens (9606) SYELTQPPSVSVSPGQTASITCSGDKLGDKYACWYQQKPGQSPVLVIYQDSKRPSGIPERFSGSNSGNTATLTISGTQAMDEADYYCQAWDSSTSYVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS |
Antigen
Chain: E
Mutation: NULL
| >8SMT_E|Chain I[auth C], J[auth E], K[auth G], L[auth K]|Spike protein S1|Severe acute respiratory syndrome coronavirus 2 (2697049) NITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPGSHHHHHH |
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)
| Chain residues position delta_SASA
: residuesposition H: ASP53 SER55 ASN56 LYS57 TYR58 TYR59 LYS64 GLY65 SER99 L: LYS27 GLY29 ASP30 LYS31 TYR32 GLN50 ASP51 SER93 SER94 E: ALA352 TRP353 ASN354 ARG355 LYS356 ARG357 ASN394 TYR396 LYS424 PRO426 ASP427 ASP428 ARG457 SER459 ASN460 LYS462 PRO463 PHE464 GLU465 ARG466 ILE468 GLU516 LEU518 HIS519 |
2、We defined interacting paratope-epitope residues by a distance cutoff of < 6 Å . Two amino acids are considered as interacting residues if they have at least one atom within a distance of 6 Å from any atom.
Interacting residues (Atom distance based)
