Closed ternary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair and phosphonoformic acid.
DOI:10.2210/pdb3kd5/pdb   NDB ID: NA0275
3KD5
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 115777.33
    Molecule: DNA (5'-D(*CP*GP*TP*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
    Polymer: 1 Type: dna Length: 18
    Chains: T
    Molecule: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(4DG))-3')
    Polymer: 2 Type: dna Length: 14
    Chains: P
    Fragment: Acyclic GMP terminated primer DNA
    Molecule: DNA polymerase
    Polymer: 3 Type: protein Length: 913
    Chains: E
    EC#: 2.7.7.7   
    Fragment: RB69 gp43 exo- chimera containing elements from the fingers domain of the human cytomegalovirus DNA polymerase.
    Mutation: D222A V478W F479V N480S I557M N558A R559L L561V I562T I563C
    Organism: Enterobacteria phage RB69
    Gene Name: 43
    UniProtKB: Protein Feature View | Search PDB | Q38087  
     
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  •   Source Hide
    Polymer: 1
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Enterobacteria phage rb69   Taxonomy   Common Name: Bacteriophage rb69 Expression System: Escherichia coli  
     
  •   Related PDB Entries Hide
    Identifier Details
    3KD1   Similar complex without phosphonoformic acid 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MG
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    MG Mg
    MAGNESIUM ION
    PPF
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    PPF C H3 O5 P
    PHOSPHONOFORMIC ACID
    PPF:3KD5
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    4DG
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    4DG C8 H12 N5 O6 P dna3PrimeTerminus
     
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  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:NA0275
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Zahn, K.E.,  Doublie, S.

    Deposition:   2009-10-22
    Release:   2011-04-13
     
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    2011-07-13
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  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.69
    R-Value: 0.219 (obs.)
    R-Free: 0.263
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 77.86 α = 90.00 
    b = 122.48 β = 90.00 
    c = 133.37 γ = 90.00