3U53

Crystal structure of human Ap4A hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of wild-type and mutant human Ap4A hydrolase

Ge, H.H.Chen, X.F.Yang, W.L.Niu, L.W.Teng, M.K.

(2013) Biochem Biophys Res Commun 432: 16-21

  • DOI: 10.1016/j.bbrc.2013.01.095
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ap4A hydrolase (asymmetrical diadenosine tetraphosphate hydrolase, EC 3.6.1.17), an enzyme involved in a number of biological processes, is characterized as cleaving the polyphosphate chain at the fourth phosphate from the bound adenosine moiety. This paper presents the crystal structure of wild-type and E58A mutant human Ap4A hydrolase ...

    Ap4A hydrolase (asymmetrical diadenosine tetraphosphate hydrolase, EC 3.6.1.17), an enzyme involved in a number of biological processes, is characterized as cleaving the polyphosphate chain at the fourth phosphate from the bound adenosine moiety. This paper presents the crystal structure of wild-type and E58A mutant human Ap4A hydrolase. Similar to the canonical Nudix fold, human Ap4A hydrolase shows the common αβα-sandwich architecture. Interestingly, two sulfate ions and one diphosphate coordinated with some conserved residues were observed in the active cleft, which affords a better understanding of a possible mode of substrate binding.


    Organizational Affiliation

    Institute of Health Sciences and Modern Experiment Technology Center, Anhui University, Hefei 230601, People's Republic of China. hhge@ahu.edu.cn



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]A, B, C, D155Homo sapiensMutation(s): 0 
Gene Names: NUDT2APAH1
EC: 3.6.1.17
Find proteins for P50583 (Homo sapiens)
Explore P50583 
Go to UniProtKB:  P50583
NIH Common Fund Data Resources
PHAROS  P50583
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.217 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.485α = 90
b = 72.485β = 90
c = 133.491γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-10-10 
  • Released Date: 2012-10-10 
  • Deposition Author(s): Ge, H.H., Teng, M.K.

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2013-03-20
    Changes: Database references