Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5649 |
| PDBID: | 7Y0W |
| Chains: | AB_R |
| Organism: | Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.42 |
| Reference: | 10.1016/j.celrep.2022.111845 |
| Antibody | |
| Antibody: | BD55-5514 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 BA.1 spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2; P0DTC2; |
Sequence information
Antibody
Heavy Chain: A
Mutation: NULL
| >7Y0W_A|Chain A|BD55-5514H|Homo sapiens (9606) QVQLVQSGAEVKKPGSSVKVSCKASGGTFRSHVISWVRQAPGQGLEWMGGFIPLFGTTIYAQAFQGRVMISADESTSTAYMELSSLRSEDTAVYFCARLFPNGDPNSPEDGFDIWGQGTLVTV |
Light Chain: B
Mutation: NULL
| >7Y0W_B|Chain B|BD55-5514L|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTITCQASQDIGNYLNWYQQKPGKAPKLLIYDASHLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQRYDDLPSYTFGQGTKVEI |
Antigen
Chain: R
Mutation: G5D/S37L/S39P/S41F/K83N/N106K/G112S/S143N/T144K/E150A/Q159R/G162S/Q164R/N167Y/Y171H/193K
| >7Y0W_R|Chain E[auth R]|Spike protein S1|Homo sapiens (9606) LCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGK |
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 A: THR28 ARG30 SER31 HIS32 VAL33 ILE52 LEU54 PHE55 THR57 PHE100 PRO101 ASN102 GLY103 ASP104 PRO105 ASN106 PHE112 B: TYR49 ASP50 HIS53 TYR91 ASP93 LEU94 PRO95 R: PRO373 PHE374 THR376 LYS378 ARG403 GLY404 ASP405 VAL407 ARG408 ASN437 ASN439 LYS440 VAL445 TYR495 SER496 ARG498 PRO499 THR500 TYR501 GLY502 VAL503 GLY504 HIS505 GLN506 TYR508 |
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)
