3VWS

Dengue serotype 3 RNA-dependent RNA polymerase bound to NITD-107

• PDB DOI: https://doi.org/10.2210/pdb3VWS/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): dengue virus type 3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-31 Released: 2013-02-27 
• Deposition Author(s): Noble, C.G., Lescar, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.224 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

Conformational flexibility of the Dengue virus RNA-dependent RNA polymerase revealed by a complex with an inhibitor

Noble, C.G., Lim, S.P., Chen, Y.L., Liew, C.W., Yap, L., Lescar, J., Shi, P.-Y.

(2013) J Virol 87: 5291-5295

• PubMed: 23408636 
• DOI: https://doi.org/10.1128/JVI.00045-13
• Primary Citation of Related Structures:  
  3VWS, 4HHJ


• PubMed Abstract: 
  

  We report a highly reproducible method to crystallize the RNA-dependent RNA polymerase (RdRp) domain of dengue virus serotype 3 (DENV-3), allowing structure refinement to a 1.79-Å resolution and revealing amino acids not seen previously. We also present a DENV-3 polymerase/inhibitor cocrystal structure at a 2.1-Å resolution. The inhibitor binds to the RdRp as a dimer and causes conformational changes in the protein. The improved crystallization conditions and new structural information should accelerate structure-based drug discovery.

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Organizational Affiliation: 

Novartis Institute for Tropical Diseases, Singapore, Singapore.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 74.59 kDa 
• Atom Count: 5,342 
• Modelled Residue Count: 592 
• Deposited Residue Count: 635 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 5	A	635	dengue virus type 3	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for Q6YMS4 (Dengue virus type 3 (strain Sri Lanka/1266/2000)) Explore Q6YMS4  Go to UniProtKB:  Q6YMS4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VWS	D [auth A], E [auth A]	5-{[(4-chlorophenyl)sulfonyl]amino}-2-methyl-1-benzofuran-3-carboxylic acid C16 H12 Cl N O5 S UZVVWRBCUSWUON-UHFFFAOYSA-N
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VWS	PDBBind:  3VWS	Kd: 2.25e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.224 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.46	α = 90
b = 177.73	β = 90
c = 57.93	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-27 
Deposition Author(s): Noble, C.G., Lescar, J.

Revision History  

• Version 1.0: 2013-02-27
  Type: Initial release
  
• Version 1.1: 2013-07-31
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description