6MJK

Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri in complex with deoxyuridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of dUTP pyrophosphatase protein, from Naegleria fowleri in complex with deoxyuridine

Delker, S.L.Abendroth, J.Lorimer, D.Edwards, T.E.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
dUTP pyrophosphatase
A
155Naegleria fowleriMutation(s): 0 
Find proteins for A0A1Z0YU86 (Naegleria fowleri)
Go to UniProtKB:  A0A1Z0YU86
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DUR
Query on DUR

Download SDF File 
Download CCD File 
A
2'-DEOXYURIDINE
C9 H12 N2 O5
MXHRCPNRJAMMIM-SHYZEUOFSA-N
 Ligand Interaction
PPV
Query on PPV

Download SDF File 
Download CCD File 
A
PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.134 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 74.230α = 90.00
b = 74.230β = 90.00
c = 74.230γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-31
    Type: Initial release