Details

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Entry information

Complex
AACDB_ID:	6636
PDBID:	3J6U
Chains:	HL_C
Organism:	dengue virus type 3, Homo sapiens
Method:	EM
Resolution (Å):	9.00
Reference:	10.1038/ncomms7341
Antibody
Antibody:	5J7 Fab
Antibody mutation:	No
INN (Clinical Trial):
Antigen
Antigen:	Dengue virus (DENV) type 3 envelope protein
Antigen mutation:	No
Durg Target:	P27915

Sequence information

Antibody

Heavy Chain: H
Mutation: NULL

>3J6U_H|Chain G[auth H]|Fab 5J7 heavy chain|Homo sapiens (9606)
WVPGSWAQVQLVQSGAELRKPGSSVKVSCRASGGTFSSYTFNWVRQAPGQGLEWMGGFIPVFNTTNYAQTFQGRVTIAADKSTSTAYMELRSLRSEDTAIYYCARDKELLFSRAFDIWGQGTMVTVSSAGTKGPS

Light Chain: L
Mutation: NULL

>3J6U_L|Chain H[auth L]|Fab 5J7 light chain|Homo sapiens (9606)
WVPGVHSDIQMTQSPSSLSASVGDRVTITCRASQSISRYLNWYQREPGKAPKLLIYGASSLQRGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSQYIPYTFGQGTKVDIKRTVA

Antigen

Chain: C
Mutation: NULL

>3J6U_C|Chain A, C, E|envelope protein|Dengue virus 3 (11069)
MRCVGVGNRDFVEGLSGATWVDVVLEHGGCVTTMAKNKPTLDIELQKTEATQLATLRKLCIEGKITNITTDSRCPTQGEAVLPEEQDQNYVCKHTYVDRGWGNGCGLFGKGSLVTCAKFQCLEPIEGKVVQYENLKYTVIITVHTGDQHQVGNETQGVTAEITPQASTTEAILPEYGTLGLECSPRTGLDFNEMILLTMKNKAWMVHRQWFFDLPLPWASGATTETPTWNRKELLVTFKNAHAKKQEVVVLGSQEGAMHTALTGATEIQNSGGTSIFAGHLKCRLKMDKLELKGMSYAMCTNTFVLKKEVSETQHGTILIKVEYKGEDAPCKIPFSTEDGQGKAHNGRLITANPVVTKKEEPVNIEAEPPFGESNIVIGIGDNALKINWYKKGSSIGKMFEATARGARRMAILGDTAWDFGSVGGVLNSLGKMVHQIFGSAYTALFSGVSWVMKIGIGVLLTWIGLNSKNTSMSFSCIAIGIITLYLGAVVQA

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)

H: SER38 TYR39 LYS107 GLU108 LEU109 LEU110

L: ASP8 TYR100 ILE101 PRO102

C: ALA50 THR51 GLN52 LEU53 THR223 THR224 GLU225 GLY273 THR274

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)

Within the threshold, the structure has no interacting amino acids and cannot be displayed. This may be due to the following reasons:
1. The method used to determine the structure is electron microscopy or nuclear magnetic resonance, which results in too low resolution;
2. the coordinates of some amino acids involved in the interaction in the structure were not detected due to technical limitations. The results are less based on atomic coordinates, but the antibody does target the antigen.

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