Details
Structure visualisation
Entry information
| Complex | |
| AACDB_ID: | 5465 |
| PDBID: | 7WT8 |
| Chains: | JI_A |
| Organism: | Severe acute respiratory syndrome coronavirus 2, Homo sapiens |
| Method: | EM |
| Resolution (Å): | 3.60 |
| 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: J
Mutation: NULL
| >7WT8_J|Chain E[auth H], G[auth J]|Heavy chain of Fab 9A8|Homo sapiens (9606) VQLVESGGGLVQPGGSLRLSCAASGIIVSSNYMSWVRQGPGKGLEWVSVIYSGGSTYYADSVKARFTISRDNSKNTLYLQMNSLRAEDTAVYYCAREVVGSNSNMDVWGQGTTVTVSSASTK |
Light Chain: I
Mutation: NULL
| >7WT8_I|Chain D, F[auth I]|light chain of Fab 9A8|Homo sapiens (9606) DIQMTQSPSSLSASVGDRVTITCQASQDINIYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTINSLQPEDIATYYCQQYDNLPRTFGQGTKVEIK |
Antigen
Chain: A
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
| >7WT8_A|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)
| I: ASP28 ILE29 ASN30 ILE31 TYR32 SER67 ASP92 ASN93 LEU94 J: VAL2 GLY26 ILE27 ILE28 SER31 ASN32 TYR33 TYR52 SER53 GLY54 SER56 TYR58 ARG97 GLY101 SER102 ASN103 SER104 ASN105 MET106 ASP107 VAL108 A: ARG400 ASP402 GLU403 ARG405 GLN406 GLN411 THR412 GLY413 ASN414 ASP417 TYR418 TYR450 LEU452 PHE453 LYS455 SER456 ASN457 TYR470 GLN471 ALA472 GLY473 ASN474 GLY482 PHE483 ASN484 CYS485 TYR486 ARG490 SER491 ARG495 THR497 TYR498 GLY499 VAL500 HIS502 |
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)
