3C5X
Crystal structure of the precursor membrane protein- envelope protein heterodimer from the dengue 2 virus at low pH
- PDB DOI: https://doi.org/10.2210/pdb3C5X/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Dengue virus 2 Thailand/16681/84, dengue virus type 2
- Expression System: Drosophila
- Mutation(s): Yes 
- Deposited: 2008-02-01 Released: 2008-04-08 
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
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Envelope protein E | 402 | Dengue virus 2 Thailand/16681/84 | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for Q6H1E5 (dengue virus type 2) Explore Q6H1E5  Go to UniProtKB:  Q6H1E5 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q6H1E5 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
prM | B [auth C] | 130 | dengue virus type 2 | Mutation(s): 3  | |
UniProt | |||||
Find proteins for Q3BCY3 (dengue virus type 2) Explore Q3BCY3  Go to UniProtKB:  Q3BCY3 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q3BCY3 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C [auth B] | 2 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G07375KG GlyCosmos:  G07375KG GlyGen:  G07375KG |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D 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 | 5 | N-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 = 71.209 | α = 90 |
b = 108.595 | β = 90 |
c = 108.738 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
PHASER | phasing |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
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