3U53

Crystal structure of human Ap4A hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.705 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.213 

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
  • Primary Citation of Related Structures:  4ICK, 4IJX

  • 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. Thi ...

    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, D
155Homo sapiensGene Names: NUDT2 (APAH1)
EC: 3.6.1.17
Find proteins for P50583 (Homo sapiens)
Go to Gene View: NUDT2
Go to UniProtKB:  P50583
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.705 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.213 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 72.485α = 90.00
b = 72.485β = 90.00
c = 133.491γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references