Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5463 |
| PDBID: | 7WT7 |
| Chains: | HD_C |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.40 |
| 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
| >7WT7_H|Chain D[auth H]|Heavy chain of Fab 9A8|Homo sapiens (9606) VQLVESGGGLVQPGGSLRLSCAASGIIVSSNYMSWVRQGPGKGLEWVSVIYSGGSTYYADSVKARFTISRDNSKNTLYLQMNSLRAEDTAVYYCAREVVGSNSNMDVWGQGTTVTVSSASTK |
Light Chain: D
Mutation: NULL
| >7WT7_D|Chain E[auth D]|Light chain of Fab 9A8|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTITCQASQDINIYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTINSLQPEDIATYYCQQYDNLPRTFGQGTKVEIK |
Antigen
Chain: C
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
| >7WT7_C|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049) MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHRAAASVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT |
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 GLU98 GLY101 SER102 ASN103 SER104 ASN105 MET106 D: GLN27 ASP28 ILE29 ASN30 ILE31 TYR32 SER67 ASP92 ASN93 LEU94 C: ARG398 ASP400 ARG403 THR410 GLY411 ASN412 ASP415 TYR416 TYR448 LEU450 PHE451 LYS453 SER454 ASN455 TYR468 ALA470 GLY471 ASN472 PHE481 ASN482 TYR484 ARG488 SER489 TYR490 SER491 THR495 TYR496 GLY497 VAL498 HIS500 |
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)
