Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5439 |
| PDBID: | 7WRL |
| Chains: | AB_R |
| Organism: | SARS coronavirus B012, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.51 |
| Reference: | 10.1038/s41586-022-04980-y |
| Antibody | |
| Antibody: | BD55-1239 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron BA.1 spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: A
Mutation: NULL
| >7WRL_A|Chain A|BD55-1239H|Homo sapiens (9606) QVQLVQSGAEVKKPGSSVKVSCKASGDIYSTYASSWVRQAPGQGLEWMGRIIPVSGTVNYADNFQGRVTITADKSTSTAYMELRSLTSEDTAVYYCARDVARGGYSGTDFFDYYYGMDVWGQGTTVT |
Light Chain: B
Mutation: NULL
| >7WRL_B|Chain B|BD55-1239L|Homo sapiens (9606) SALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPDKAPKLLIYDVNNRPSGVSTRFSGSKSGNTASLTISRLQTDDEADYSCSSYTSSNTWVFGGGTK |
Antigen
Chain: R
Mutation: G6D/S38L/S40P/S42F/K84N/N107K/G113S/S144N/T145K/E151A/Q160R/G163S/Q165R/N168Y/Y172H
| >7WRL_R|Chain C[auth R]|Spike protein S1|SARS coronavirus B012 (305406) NLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCG |
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)
| A: VAL54 SER55 THR57 ASN59 LYS74 ARG102 GLY104 TYR105 SER106 GLY107 THR108 ASP109 PHE110 PHE111 ASP112 TYR114 B: SER27 TYR32 TYR34 TYR93 SER95 SER96 ASN97 R: TYR369 ASN370 ALA372 PHE374 PHE375 THR376 PHE377 LYS378 CYS379 TYR380 VAL382 SER383 PRO384 GLY404 ASP405 VAL407 ARG408 GLN414 TYR501 GLY502 VAL503 GLY504 HIS505 TYR508 |
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)
