3C5X

Crystal structure of the precursor membrane protein- envelope protein heterodimer from the dengue 2 virus at low pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope protein E402Dengue virus 2 Thailand/16681/84Mutation(s): 0 
UniProt
Find proteins for Q6H1E5 (dengue virus type 2)
Explore Q6H1E5 
Go to UniProtKB:  Q6H1E5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6H1E5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
prMB [auth C]130dengue virus type 2Mutation(s): 3 
UniProt
Find proteins for Q3BCY3 (dengue virus type 2)
Explore Q3BCY3 
Go to UniProtKB:  Q3BCY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3BCY3
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth B]2N/A
Glycosylation Resources
GlyTouCan:  G07375KG
GlyCosmos:  G07375KG
GlyGen:  G07375KG
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-altropyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G43142BR
GlyCosmos:  G43142BR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.209α = 90
b = 108.595β = 90
c = 108.738γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2008-04-08 
  • Deposition Author(s): Li, L.

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2011-08-24
    Changes: Atomic model
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references, Derived calculations, Structure summary
  • Version 2.2: 2023-08-30
    Changes: Data collection, Refinement description