2FOM

Dengue Virus NS2B/NS3 Protease

• PDB DOI: https://doi.org/10.2210/pdb2FOM/pdb

• Classification: VIRAL PROTEIN/PROTEASE
• Organism(s): dengue virus type 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-01-13 Released: 2006-03-07 
• Deposition Author(s): Schiering, N., Kroemer, M., Renatus, M., Erbel, P., D'Arcy, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.209 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Starting Model: experimental

Literature

Structural basis for the activation of flaviviral NS3 proteases from dengue and West Nile virus.

Erbel, P., Schiering, N., D'Arcy, A., Renatus, M., Kroemer, M., Lim, S.P., Yin, Z., Keller, T.H., Vasudevan, S.G., Hommel, U.

(2006) Nat Struct Mol Biol 13: 372-373

• PubMed: 16532006 
• DOI: https://doi.org/10.1038/nsmb1073
• Primary Citation of Related Structures:  
  2FOM, 2FP7


• PubMed Abstract: 
  

  The replication of flaviviruses requires the correct processing of their polyprotein by the viral NS3 protease (NS3pro). Essential for the activation of NS3pro is a 47-residue region of NS2B. Here we report the crystal structures of a dengue NS2B-NS3pro complex and a West Nile virus NS2B-NS3pro complex with a substrate-based inhibitor. These structures identify key residues for NS3pro substrate recognition and clarify the mechanism of NS3pro activation.

---

Organizational Affiliation: 

Novartis Institutes for Biomedical Research, Protease Platform, 4002 Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.57 kDa 
• Atom Count: 1,718 
• Modelled Residue Count: 196 
• Deposited Residue Count: 247 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
polyprotein	A	62	dengue virus type 2	Mutation(s): 0
UniProt
Find proteins for Q91H74 (dengue virus type 2) Explore Q91H74  Go to UniProtKB:  Q91H74

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
polyprotein	B	185	dengue virus type 2	Mutation(s): 0  EC: 3.4.21.91
UniProt
Find proteins for Q91H74 (dengue virus type 2) Explore Q91H74  Go to UniProtKB:  Q91H74

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth B], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.209 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.307	α = 90
b = 61.109	β = 90
c = 113.877	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-07 
Deposition Author(s): Schiering, N., Kroemer, M., Renatus, M., Erbel, P., D'Arcy, A.

Revision History  

• Version 1.0: 2006-03-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-02-14
  Changes: Experimental preparation
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.6: 2024-04-03
  Changes: Refinement description