3EHW

Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site

Takacs, E.Barabas, O.Vertessy, B.G.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
dUTP pyrophosphatase164Homo sapiensMutation(s): 0 
Gene Names: DUT
EC: 3.6.1.23
UniProt & NIH Common Fund Data Resources
Find proteins for P33316 (Homo sapiens)
Explore P33316 
Go to UniProtKB:  P33316
PHAROS:  P33316
GTEx:  ENSG00000128951 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33316
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DUP
Query on DUP

Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
L [auth C]
O [auth X]
R [auth Y]
H [auth A],
K [auth B],
L [auth C],
O [auth X],
R [auth Y],
T [auth Z]
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]
I [auth A]
J [auth B]
M [auth C]
N [auth X]
G [auth A],
I [auth A],
J [auth B],
M [auth C],
N [auth X],
P [auth X],
Q [auth Y],
S [auth Z]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
DUP PDBBind:  3EHW IC50: 1.52e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.446α = 90
b = 87.16β = 90.09
c = 70.608γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-03-07
    Changes: Database references
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description