Details

Structure visualisation

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Entry information

Complex
AACDB_ID: 6380
PDBID: 8HHY
Chains: FW_B
Organism: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Method: EM
Resolution (Å): 2.77
Reference: 10.1038/s41467-023-35949-8
Antibody
Antibody: IS-9A Fab
Antibody mutation: No
INN (Clinical Trial):
Antigen
Antigen: SARS-CoV-2 Delta spike glycoprotein
Antigen mutation: Yes
Durg Target: P0DTC2

Sequence information

Antibody

Heavy Chain: F
Mutation: NULL

>8HHY_F|Chain A[auth F], C[auth G], E[auth H]|IS-9A Fab heavy chain|Homo sapiens (9606)
QVQLVQSGAEVKKPGESLRISCKGSGYSFTNYWISWVRQMPGKGLEWMGRIDPSDSYINYSPSFQGHATISADKSISTAYLQWGSLKASDTAMYYCARGRNYLDSRGRFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Light Chain: W
Mutation: NULL

>8HHY_W|Chain B[auth I], D[auth L], F[auth W]|IS-9A Fab light chain|Homo sapiens (9606)
DIVMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKSGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDSLGFTFGPGTKVEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Antigen

Chain: B
Mutation: T25R/G148D/E162G/N456R/G482K/Y618G/N685R/S686G/P687S/R689G/L954N/D991P/K992E

>8HHY_B|Chain G[auth A], H[auth B], I[auth C]|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049)
MKVKLLVLLCTFTATYAGTQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGSKPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSRGSAGSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQNVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQDIRSLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH

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)

F: THR30 ASN31 ARG50 SER54 ASP55 TYR57 ASN59 PRO62 PHE64 ARG100 TYR102 LEU103 ASP104 SER105 ARG106

W: GLN27 ASP28 SER30 TYR32 GLN90 ASP92 SER93 LEU94

B: VAL367 LEU368 TYR369 ASN370 SER371 ALA372 SER373 PHE374 SER375 PHE377 LYS378 CYS379 TYR380 THR385 GLY404 ASP405 ARG408 ALA411 ASN437 VAL503 GLY504 GLN506 TYR508

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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