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Entry information

Complex
AACDB_ID: 4867
PDBID: 7SD3
Chains: NK_B
Organism: Homo sapiens, HIV whole-genome vector AA1305#18
Method: EM
Resolution (Å): 3.67
Reference: 10.1038/s41467-022-34008-y
Antibody
Antibody: 4E10 Fab
Antibody mutation: No
INN (Clinical Trial):
Antigen
Antigen: HIV-1 envelope glycoprotein - gp41
Antigen mutation: No
Durg Target:

Sequence information

Antibody

Heavy Chain: N
Mutation: NULL

>7SD3_N|Chain A[auth H], C[auth M], E[auth N]|4E10 Fab light chain|Homo sapiens (9606)
EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Light Chain: K
Mutation: NULL

>7SD3_K|Chain B[auth G], D[auth I], F[auth K]|4E10 Fab heavy chain|Homo sapiens (9606)
QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGWGWLGKPIGAFAHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Antigen

Chain: B
Mutation: NULL

>7SD3_B|Chain H[auth B], J[auth D], L[auth F]|Transmembrane protein gp41|HIV whole-genome vector AA1305#18 (672471)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALDKWASLWNWFDISNWLWYIKL

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)

N: LYS32 TYR91 GLY92 GLN93 SER94

K: SER28 THR31 TYR32 ALA33 TRP47 LEU53 LEU54 ASN58 GLU95

B: TRP666 TRP670 ASN671 TRP672 PHE673 ASP674 ILE675 SER676 ASN677 TRP678 LEU679 TRP680 LYS683 LEU684

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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