RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dGTP Opposite Difluorotoluene Nucleoside
DOI:10.2210/pdb3qes/pdb   NDB ID: NA0955
3QES
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 114685.83
    Molecule: DNA polymerase
    Polymer: 1 Type: protein Length: 903
    Chains: A
    EC#: 2.7.7.7   
    Mutation: D222A, D327A, L561A, S565G, Y567A
    Organism: Enterobacteria phage RB69
    Gene Name: 43
    UniProtKB: Search PDB | Q38087   Protein Feature View
    Molecule: DNA (5'-D(*TP*CP*GP*(DFT)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
    Polymer: 2 Type: dna Length: 18
    Chains: T
    Details: DNA Template
    Molecule: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3')
    Polymer: 3 Type: dna Length: 13
    Chains: P
    Details: DNA Primer
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Enterobacteria phage rb69   Taxonomy   Common Name: Bacteriophage rb69 Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3QEI    
    3QEP    
    3QER    
    3QET    
    3QEV    
    3QEW    
    3QEX    
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    CA
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    Download 
    CA Ca
    CALCIUM ION
    DGT
    Search 
    Download 
    DGT C10 H16 N5 O13 P3
    2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
    DGT:3QES
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    DFT
    Search 
    DFT C12 H15 F2 O6 P dnaLinking
    DOC
    Search 
    DOC C9 H14 N3 O6 P DC dnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:NA0955
     
 
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:   Xia, S.,  Konigsberg, W.H.,  Wang, J.

    Deposition:   2011-01-20
    Release:   2012-01-25
    Last Modified (REVDAT):   2012-03-14
     
  •   Revision History    Hide
    Mouse over text for details
    2012-03-14
    Citation
    2012-02-22
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   1.98
    R-Value: 0.179 (obs.)
    R-Free: 0.218
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 74.82 α = 90.00 
    b = 119.98 β = 90.00 
    c = 130.07 γ = 90.00