5QJL

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z56983806


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-sugar pyrophosphatase
A, B, C, D
209Homo sapiensMutation(s): 0 
Gene Names: NUDT5NUDIX5HSPC115
EC: 3.6.1.13 (PDB Primary Data), 3.6.1.58 (PDB Primary Data), 2.7.7.96 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKK9 (Homo sapiens)
Explore Q9UKK9 
Go to UniProtKB:  Q9UKK9
PHAROS:  Q9UKK9
GTEx:  ENSG00000165609 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKK9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JJM
Query on JJM

Download Ideal Coordinates CCD File 
M [auth B],
N [auth B],
S [auth C],
W [auth D]
1-methyl-N-(3-methylphenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
C13 H13 N5
MLUHWTUFJZKUST-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth B]
O [auth B]
P [auth C]
H [auth A],
I [auth A],
J [auth B],
O [auth B],
P [auth C],
T [auth C],
X [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
K [auth B]
L [auth B]
Q [auth C]
E [auth A],
F [auth A],
K [auth B],
L [auth B],
Q [auth C],
R [auth C],
U [auth D],
V [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.89α = 79.68
b = 59.51β = 82.07
c = 79.98γ = 76.2
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-10-30
    Changes: Structure summary