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Topoisomerase II-DNA-AMPPNP complex
DOI:10.2210/pdb4gfh/pdb   NDB ID: NA1991
4GFH
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Isomerase/dna
    Structure Weight: 305580.15
    Molecule: DNA topoisomerase 2
    Polymer: 1 Type: protein Length: 1177
    Chains: A, F
    EC#: 5.99.1.3   
    Fragment: UNP RESIDUES 1-1177
    Organism Saccharomyces cerevisiae S288c
    Gene Names TOP2 TOR3 YNL088W N2244
    UniProtKB:   Protein Feature View | Search PDB | P06786  
    Molecule: DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3')
    Polymer: 2 Type: dna Length: 11
    Chains: B, G
    Molecule: DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3')
    Polymer: 3 Type: dna Length: 15
    Chains: C, H
    Molecule: DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*(TSP))-3')
    Polymer: 4 Type: dna Length: 11
    Chains: D, I
    Molecule: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3')
    Polymer: 5 Type: dna Length: 15
    Chains: E, J
     
  •   Structure Validation Hide

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  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 4
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 5
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    1PVG  yeast ATPase 
    3L4J  yeast DNA binding and cleavage core 
    3L4K  yeast DNA binding and cleavage core 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    ANP
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    ANP C10 H17 N6 O12 P3
    PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
    MG
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    MG Mg
    MAGNESIUM ION
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    PTR
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    PTR C9 H12 N O6 P TYR lPeptideLinking
    TSP
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    TSP C10 H15 N2 O7 P S T nonPolymer
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA1991
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors
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  •   Deposition Summary Hide
    Authors:   Schmidt, B.H.,  Osheroff, N.,  Berger, J.M.

    Deposition:   2012-08-03
    Release:   2012-10-03
    Last Modified (REVDAT):   2012-12-12
     
  •   Revision History    Hide
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    2012-12-12
    Citation
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   4.41
    R-Value: 0.241 (obs.)
    R-Free: 0.275
    Space Group: P 21 21 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 169.13 α = 90.00 
    b = 169.88 β = 90.00 
    c = 169.21 γ = 90.00