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RB69 DNA Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with dUpCpp Opposite dA
DOI:10.2210/pdb3spy/pdb   NDB ID: NA1203
3SPY
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna
    Structure Weight: 114283.96
    Molecule: DNA polymerase
    Polymer: 1 Type: protein Length: 901
    Chains: A
    EC#: 2.7.7.7   
    Mutation: L415A, L561A, S565G, Y567A
    Organism: Enterobacteria phage RB69
    Gene Name: 43
    UniProtKB: Protein Feature View | Search PDB | Q38087  
    Molecule: 5'-D(*TP*CP*GP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'
    Polymer: 2 Type: dna Length: 18
    Chains: T
    Details: template
    Molecule: 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3'
    Polymer: 3 Type: dna Length: 13
    Chains: P
    Details: 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   Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3SPZ  RB69 DNA Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with dUpCpp Opposite dA (Ca2+) 
    3SQ0  RB69 DNA Polymerase(L561A/S565G/Y567A) Ternary Complex with dUpNpp Opposite dA (Mn2+) 
    3SQ1  RB69 DNA Polymerase Ternary Complex with dUpCpp Opposite dA 
    3SQ2  RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (AT rich sequence) 
    3SQ4  RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (GC rich sequence) 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MG
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    MG Mg
    MAGNESIUM ION
    UPC
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    UPC C10 H17 N2 O13 P3
    2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine
    UPC:3SPY
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA1203
     
 
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:   2011-07-04
    Release:   2011-10-12
    Last Modified (REVDAT):   2011-11-02
     
  •   Revision History    Hide
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    2011-11-02
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.14
    R-Value: 0.194 (obs.)
    R-Free: 0.242
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 75.34 α = 90.00 
    b = 120.60 β = 90.00 
    c = 130.81 γ = 90.00