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Entry information

Complex
AACDB_ID: 5341
PDBID: 7WHD
Chains: JK_B
Organism: Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Method: EM
Resolution (Å): 2.65
Reference: 10.1080/22221751.2023.2245921
Antibody
Antibody: B8 Fab
Antibody mutation: No
INN (Clinical Trial):
Antigen
Antigen: SARS-CoV-2 spike glycoprotein
Antigen mutation: Yes
Durg Target: P0DTC2

Sequence information

Antibody

Heavy Chain: J
Mutation: NULL

>7WHD_J|Chain D, F[auth G], H[auth J]|antibody ZB8 heavy chain|Homo sapiens (9606)
EVQLVQSGAEVKKPGSSVKVSCKASGGTFSNYGISWVRQAPGQGLEWMGRILPTFGTANSAQKFQGRVTITADESTGTAYMELRSLRSEDTAVYYCAKEGLAFLGYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Light Chain: K
Mutation: NULL

>7WHD_K|Chain E, G[auth H], I[auth K]|antibody ZB8 light chain|Homo sapiens (9606)
EIVLTQSPGTLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFIGSGSGTDFTLTISSLEPEDFAVYFCQQRSNWPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Antigen

Chain: B
Mutation: K960P/V961P

>7WHD_B|Chain A, B, C|Spike glycoprotein|Severe acute respiratory syndrome coronavirus 2 (2697049)
AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD

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)

J: GLU1 SER30 ASN31 TYR32 ARG50 LEU52 PHE55 THR57 ALA58 ASN59 LYS98 GLY100 LEU101 ALA102 PHE103 LEU104 GLY105 TYR106 ASP109

K: TYR32 TYR49 ASN53 THR56 SER92 ASN93 TRP94

B: TYR351 LYS444 VAL445 GLY446 TYR449 ASN450 LEU452 LEU455 PHE456 THR470 ILE472 GLY482 VAL483 GLU484 GLY485 PHE486 ASN487 TYR489 PHE490 LEU492 GLN493 SER494 GLY496 GLN498 THR500 ASN501 TYR505

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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