5QJ5

PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with Z44592329


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-sugar pyrophosphatase
A, B, C, D
209Homo sapiensMutation(s): 0 
Gene Names: NUDT5 (NUDIX5)
EC: 3.6.1.13
Find proteins for Q9UKK9 (Homo sapiens)
Go to Gene View: NUDT5
Go to UniProtKB:  Q9UKK9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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

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Download CCD File 
B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
K0G
Query on K0G

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Download CCD File 
A, B, C, D
N-phenyl-N'-pyridin-3-ylurea
C12 H11 N3 O
WBKYYDBHEGTTON-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.215 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.146α = 79.47
b = 59.774β = 81.89
c = 80.086γ = 75.78
Software Package:
Software NamePurpose
REFMACphasing
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release