5QJA

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z1497321453


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)

Dubianok, Y.Collins, P.Krojer, T.Wright, N.Strain-Damerell, C.Burgess-Brown, N.Bountra, C.Arrowsmith, C.H.Edwards, A.Huber, K.von Delft, F.

To be published.

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

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

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Download CCD File 
A, B, C, D
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
K0A
Query on K0A

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Download CCD File 
A, B, D
(2,5-dimethyl-1,3-thiazol-4-yl)(pyrrolidin-1-yl)methanone
C10 H14 N2 O S
BRAPKXFMPGACJU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.437α = 79.33
b = 59.840β = 81.51
c = 80.189γ = 75.50
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
REFMACphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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