5IKM

1.9 Angstrom Crystal Structure of NS5 Methyl Transferase from Dengue Virus 1 in Complex with S-Adenosylmethionine and Beta-D-Fructopyranose.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

1.9 Angstrom Crystal Structure of NS5 Methyl Transferase from Dengue Virus 1 in Complex with S-Adenosylmethionine and Beta-D-Fructopyranose.

Minasov, G.Shuvalova, L.Winsor, J.Dubrovska, I.Flores, K.Shatsman, S.Kwon, K.Anderson, W.F.Center for Structural Genomics of Infectious Diseases

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NS5 Methyl Transferase
A
269Dengue virus 1Mutation(s): 0 
Find proteins for I6XG39 (Dengue virus 1)
Go to UniProtKB:  I6XG39
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MLT
Query on MLT

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A
D-MALATE
(2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BDF
Query on BDF

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Download CCD File 
A
BETA-D-FRUCTOPYRANOSE
C6 H12 O6
LKDRXBCSQODPBY-ARQDHWQXSA-N
 Ligand Interaction
SAM
Query on SAM

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Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 58.380α = 90.00
b = 86.230β = 90.00
c = 144.307γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MoRDaphasing
HKL-3000data scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Derived calculations, Refinement description