Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5595 |
| PDBID: | 7XDB |
| Chains: | ED_A |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 2.62 |
| Reference: | 10.1038/s41421-022-00509-9 |
| Antibody | |
| Antibody: | BA7208 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron spike glycoprotein |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: E
Mutation: NULL
| >7XDB_E|Chain A[auth E], E[auth F], H|BA7208 fab|Homo sapiens (9606) DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASSLESGVPSRFSGSGSGTEFTLTITSLQPDDFATYYCQQYDSFSWTFGQGTKLEI |
Light Chain: D
Mutation: NULL
| >7XDB_D|Chain C[auth D], D[auth G], I|BA7208 fab|Homo sapiens (9606) VQLVQSGAEVKKPGESLKISCKGSGYSFTSYYWIGWVRQMPGKGLEWMGIVYPDDSDTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYCVRHPGGGDWYFDLWGRGTLVTV |
Antigen
Chain: A
Mutation: A42V/A68I/F115D/181I/G311D/S343L/S345P/S347F/K389N/N412K/G418S/S449N/T450K/E456A/Q465R/G468S/Q470R/N473Y/Y477H/T519K/D586G/H627Y/N736K/D768Y/F789P/N828K/A864P/A871P/A914P/Q926H/N941K/L953F/K958P/V959P
| >7XDB_A|Chain B[auth A], F[auth B], G[auth C]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) PAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPE |
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)
| E: TRP32 TYR91 ASP92 SER93 PHE94 D: SER28 PHE29 TYR32 TYR33 TRP34 TYR53 ASP55 ASP56 ASP58 ARG60 PRO101 GLY102 GLY103 GLY104 ASP105 TRP106 A: ASN343 THR345 ARG346 ASN439 LYS440 LEU441 ASP442 SER443 LYS444 VAL445 SER446 ASN448 ASN450 PRO499 THR500 |
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)
