6XD1

Dengue serotype 3 RNA-dependent RNA polymerase bound to NITD-640


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Dengue serotype 3 RNA-dependent RNA polymerase bound to NITD-640

Arora, R.Benson, T.E.Liew, C.W.Lescar, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-dependent RNA polymeraseA635Dengue virus 3Mutation(s): 0 
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for Q6YMS4 (Dengue virus type 3 (strain Sri Lanka/1266/2000))
Explore Q6YMS4 
Go to UniProtKB:  Q6YMS4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V0J
Query on V0J

Download Ideal Coordinates CCD File 
D [auth A](2R)-4-(butyl{[2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]methyl}carbamoyl)-1-(2,2-diphenylpropanoyl)piperazine-2-carboxylic acid
C39 H41 N7 O4
CKFCJCLSPLLPGD-UUWRZZSWSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.533α = 90
b = 175.198β = 90
c = 57.748γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release