Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA and dGTP
DOI:10.2210/pdb4fyd/pdb   NDB ID: NA1921
4FYD
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 230933.21
    Molecule: DNA polymerase alpha catalytic subunit A
    Polymer: 1 Type: protein Length: 910
    Chains: A, B
    EC#: 2.7.7.7   
    Fragment: Polymerase domain, UNP residues 349-1258
    Mutation: R508A, N509A, D998N
    Organism: Saccharomyces cerevisiae S288c
    Gene Names: POL1 CDC17 YNL102W N2181
    UniProtKB: Protein Feature View | Search PDB | P13382  
    Molecule: DNA (5'-D(*TP*GP*AP*GP*CP*GP*TP*G*TP*GP*TP*AP*CP*CP*CP*CP*TP*GP*CP*CP*CP*GP*CP*CP*G)-3')
    Polymer: 2 Type: dna Length: 25
    Chains: C, D
    Molecule: DNA/RNA (5'-R(*CP*GP*GP*CP*GP*GP*GP*CP*AP*G)-D(P*GP*G)-3')
    Polymer: 3 Type: hybrid Length: 12
    Chains: E, F
     
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  •   Source Hide
    Polymer: 1
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    4B08   Crystal structure of yeast DNA polymerase alpha, selenomethionine protein 
    4FVM   Crystal structure of yeast DNA polymerase alpha 
    4FXD   Crystal structure of yeast DNA polymerase alpha bound to DNA/RNA 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    DGT
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    DGT C10 H16 N5 O13 P3
    2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
     
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  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:NA1921
     
 
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:   Perera, R.L.,  Pellegrini, L.

    Deposition:   2012-07-04
    Release:   2013-02-27
    Last Modified (REVDAT):   2014-01-15
     
  •   Revision History    Hide
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    2014-01-15
    Citation
    2013-04-24
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   3.10
    R-Value: 0.212 (obs.)
    R-Free: 0.247
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 111.69 α = 90.00 
    b = 145.69 β = 90.00 
    c = 197.20 γ = 90.00