Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5466 |
| PDBID: | 7WT9 |
| Chains: | HA_E |
| Organism: | Homo sapiens, Severe acute respiratory syndrome coronavirus 2 |
| Method: | EM |
| Resolution (Å): | 4.30 |
| Reference: | 10.1038/s41421-022-00443-w |
| Antibody | |
| Antibody: | 9A8 Fab |
| Antibody mutation: | No |
| INN (Clinical Trial): | |
| Antigen | |
| Antigen: | SARS-CoV-2 Omicron spike glycoprotein RBD |
| Antigen mutation: | Yes |
| Durg Target: | P0DTC2 |
Sequence information
Antibody
Heavy Chain: H
Mutation: NULL
| >7WT9_H|Chain A[auth H]|Heavy chain of Fab 9A8|Homo sapiens (9606) VQLVESGGGLVQPGGSLRLSCAASGIIVSSNYMSWVRQGPGKGLEWVSVIYSGGSTYYADSVKARFTISRDNSKNTLYLQMNSLRAEDTAVYYCAREVVGSNSNMDVWGQGTTVTVSSASTK |
Light Chain: A
Mutation: NULL
| >7WT9_A|Chain C[auth A]|Light chain of Fab 9A8|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTITCQASQDINIYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTINSLQPEDIATYYCQQYDNLPRTFGQGTKVEIK |
Antigen
Chain: E
Mutation: A67V/A93I/F140D/H207I/G337D/S369L/S371P/S373F/K415N/N438K/G444S/S475N/T476K/E482A/Q491R/G494S/Q496R/N499Y/Y503H/T545K/D612G/H653Y/N677K/P679H/R680G/R681A/R683A/N762K/D794Y/F815P/N854K/A890P/A897P/A940P/Q952H/N967K/L979F/K984P/V985P
| >7WT9_E|Chain B[auth E]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHRAAASVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT |
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)
| H: VAL2 GLY26 ILE27 ILE28 SER31 ASN32 TYR33 TYR52 SER53 GLY54 SER56 TYR58 ASN76 ARG97 GLU98 GLY101 SER102 ASN103 SER104 ASN105 MET106 A: GLN27 ASP28 ILE29 ASN30 ILE31 TYR32 SER67 ASP92 ASN93 LEU94 E: ARG403 ASP405 GLU406 ARG408 GLN414 THR415 GLY416 ASN417 ASP420 TYR421 TYR453 LEU455 PHE456 LYS458 SER459 ASN460 TYR473 GLN474 ALA475 GLY476 ASN477 PHE486 ASN487 TYR489 ARG493 SER494 TYR495 SER496 THR500 TYR501 GLY502 VAL503 HIS505 |
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)
