3VWS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1128/JVI.00045-13
  • Primary Citation of Related Structures:  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 pres ...

    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.


    Organizational Affiliation

    Novartis Institute for Tropical Diseases, Singapore, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Non-structural protein 5
A
635Dengue virus type 3 (strain Sri Lanka/1266/2000)Gene Names: pol
EC: 3.6.1.15, 2.1.1.56, 2.1.1.57, 3.4.21.91, 3.6.4.13, 2.7.7.48
Find proteins for Q6YMS4 (Dengue virus type 3 (strain Sri Lanka/1266/2000))
Go to UniProtKB:  Q6YMS4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
VWS
Query on VWS

Download SDF File 
Download CCD File 
A
5-{[(4-chlorophenyl)sulfonyl]amino}-2-methyl-1-benzofuran-3-carboxylic acid
C16 H12 Cl N O5 S
UZVVWRBCUSWUON-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VWSKd: 225000 nM BINDINGMOAD
VWSKd: 225000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 161.460α = 90.00
b = 177.730β = 90.00
c = 57.930γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
BUSTERrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-07-31
    Type: Database references