1OKE

Crystal structure of the dengue 2 virus envelope protein in complex with n-octyl-beta-D-glucoside

• PDB DOI: https://doi.org/10.2210/pdb1OKE/pdb
• Entry: 1OKE supersedes: 1OAM

• Classification: VIRAL PROTEIN
• Organism(s): dengue virus type 2
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2003-07-22 Released: 2003-07-24 
• Deposition Author(s): Modis, Y., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.294 
• R-Value Work: 0.263 
• R-Value Observed: 0.263 

Literature

A Ligand-Binding Pocket in the Dengue Virus Envelope Glycoprotein.

Modis, Y., Ogata, S., Clements, D., Harrison, S.C.

(2003) Proc Natl Acad Sci U S A 100: 6986

• PubMed: 12759475 
• DOI: https://doi.org/10.1073/pnas.0832193100
• Primary Citation of Related Structures:  
  1OAN, 1OKE


• PubMed Abstract: 
  

  Dengue virus is an emerging global health threat. Its major envelope glycoprotein, E, mediates viral attachment and entry by membrane fusion. A crystal structure of the soluble ectodomain of E from dengue virus type 2 reveals a hydrophobic pocket lined by residues that influence the pH threshold for fusion. The pocket, which accepts a hydrophobic ligand, opens and closes through a conformational shift in a beta-hairpin at the interface between two domains. These features point to a structural pathway for the fusion-activating transition and suggest a strategy for finding small-molecule inhibitors of dengue and other flaviviruses.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Children's Hospital and Harvard Medical School, 320 Longwood Avenue, Boston, MA 02115, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 90.13 kDa 
• Atom Count: 6,426 
• Modelled Residue Count: 788 
• Deposited Residue Count: 788 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAJOR ENVELOPE PROTEIN E	A, B	394	dengue virus type 2	Mutation(s): 0
UniProt
Find proteins for P12823 (Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969)) Explore P12823  Go to UniProtKB:  P12823
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86566TX GlyCosmos:  G86566TX GlyGen:  G86566TX

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	F [auth A], H [auth B]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
NAG	E [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.294 
• R-Value Work: 0.263 
• R-Value Observed: 0.263 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.602	α = 90
b = 81.602	β = 90
c = 287.408	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-24 
Deposition Author(s): Modis, Y., Harrison, S.C.
• This entry supersedes: 1OAM

Revision History  

• Version 1.0: 2003-07-24
  Type: Initial release
  
• Version 1.1: 2012-01-18
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2024-11-06
  Changes: Data collection, Database references, Structure summary