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Human Aprataxin (Aptx) bound to RNA-DNA and Zn - adenosine vanadate transition state mimic complex
DOI:10.2210/pdb4ndg/pdb   NDB ID: NA2747
4NDG
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: DNA Binding Protein/rna/dna
    Structure Weight: 55557.13
    Molecule: Aprataxin
    Polymer: 1 Type: protein Length: 182
    Chains: A, B
    EC#: 3   
    Organism Homo sapiens
    Gene Names APTX AXA1
    UniProtKB:   Protein Feature View | Search PDB | Q7Z2E3  
    Molecule: 5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3'
    Polymer: 2 Type: hybrid Length: 10
    Chains: D, G
    Molecule: 5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3'
    Polymer: 3 Type: dna Length: 10
    Chains: E, H
     
  •   Structure Validation Hide

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  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3SZQ   
    4NDF   
    4NDH   
    4NDI   
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    V5A
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    V5A C10 H13 N5 O6 V
    adenosine-5'-vanadate
    V5A:4NDG
    ZN
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    ZN Zn
    ZINC ION
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA2747
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly 1       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Schellenberg, M.J.,  Tumbale, P.S.,  Williams, R.S.

    Deposition:   2013-10-26
    Release:   2013-12-18
    Last Modified (REVDAT):   2014-02-05
     
  •   Revision History    Hide
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    2014-02-05
    Citation
    2014-01-15
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   2.54
    R-Value: 0.211 (obs.)
    R-Free: 0.260
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 40.28 α = 90.00 
    b = 114.58 β = 90.00 
    c = 124.66 γ = 90.00