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Entry information

Complex
AACDB_ID: 5464
PDBID: 7WT8
Chains: HD_C
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: H
Mutation: NULL

>7WT8_H|Chain E[auth H], G[auth J]|Heavy chain of Fab 9A8|Homo sapiens (9606)
VQLVESGGGLVQPGGSLRLSCAASGIIVSSNYMSWVRQGPGKGLEWVSVIYSGGSTYYADSVKARFTISRDNSKNTLYLQMNSLRAEDTAVYYCAREVVGSNSNMDVWGQGTTVTVSSASTK

Light Chain: D
Mutation: NULL

>7WT8_D|Chain D, F[auth I]|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

>7WT8_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)

D: ASP28 ASN30 ILE31 TYR32 SER67 GLY68 ASP92 ASN93 LEU94

H: VAL2 GLY26 ILE27 ILE28 SER31 ASN32 TYR33 TYR52 SER53 GLY54 SER56 TYR58 ASN76 ARG97 GLU98 GLY101 SER102 ASN103 SER104 ASN105 MET106 ASP107

C: ARG398 ASP400 ARG403 GLN404 GLN409 THR410 GLY411 ASN412 ASP415 TYR416 TYR448 LEU450 PHE451 LYS453 SER454 ASN455 TYR468 GLN469 ALA470 GLY471 ASN472 GLY480 PHE481 ASN482 CYS483 TYR484 ARG488 SER489 SER491 THR495 TYR496 GLY497 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)

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