Crystal structure of human AP4A hydrolase E58A mutant

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

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This is version 1.2 of the entry. See complete history


Crystal structure of wild-type and mutant human Ap4A hydrolase.

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

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

  • DOI: https://doi.org/10.1016/j.bbrc.2013.01.095
  • Primary Citation of Related Structures:  
    3U53, 4ICK, 4IJX

  • PubMed Abstract: 

    Ap4A hydrolase (asymmetrical diadenosine tetraphosphate hydrolase, EC, 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
A, B
155Homo sapiensMutation(s): 1 
Gene Names: NUDT2APAH1
UniProt & NIH Common Fund Data Resources
Find proteins for P50583 (Homo sapiens)
Explore P50583 
Go to UniProtKB:  P50583
PHAROS:  P50583
GTEx:  ENSG00000164978 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50583
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.19α = 90
b = 72.19β = 90
c = 133.51γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Advisory, Refinement description
  • Version 1.2: 2023-11-08
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description