Quinazolinedione-DNA cleavage complex of type IV topoisomerase from S. pneumoniae
DOI:10.2210/pdb3raf/pdb   NDB ID: NA1061
3RAF
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Isomerase/dna/antibiotic
    Structure Weight: 185505.42
    Molecule: DNA topoisomerase 4 subunit A
    Polymer: 1 Type: protein Length: 496
    Chains: A, B
    EC#: 5.99.1.3   
    Fragment: UNP residues 1-488
    Organism: Streptococcus pneumoniae
    Gene Names: parC SP_0855
    UniProtKB: Protein Feature View | Search PDB | P72525  
    Molecule: DNA topoisomerase 4 subunit B
    Polymer: 2 Type: protein Length: 268
    Chains: C, D
    EC#: 5.99.1.3   
    Fragment: UNP residues 404-647
    Organism: Streptococcus pneumoniae
    Gene Names: parE SP_0852
    UniProtKB: Protein Feature View | Search PDB | Q59961  
    Molecule: 5'-D(*CP*AP*TP*GP*AP*AP*T)-3'
    Polymer: 3 Type: dna Length: 7
    Chains: E
    Molecule: 5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*G)-3'
    Polymer: 4 Type: dna Length: 11
    Chains: F
    Molecule: 5'-D(*CP*GP*TP*GP*CP*AP*T)-3'
    Polymer: 5 Type: dna Length: 7
    Chains: G
    Molecule: 5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*G)-3'
    Polymer: 6 Type: dna Length: 11
    Chains: H
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Streptococcus pneumoniae   Taxonomy   Expression System: Escherichia coli  
    Polymer: 2
    Scientific Name: Streptococcus pneumoniae   Taxonomy   Expression System: Escherichia coli  
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 4
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 5
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 6
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    2NOV   Crystal structure of ParC55 from S. pneumoniae 
    3FOE   Clinafloxacin-stabilised cleavage complex of topo IV from S. pneumoniae 
    3FOF   Moxifloxacin-stabilised cleavage complex of topo IV from S. pneumoniae 
    3K9F   Levofloxacin-stabilised cleavage complex of topo IV from S. pneumoniae (soaked) 
    3KSA   Drug-free cleavage complex of topo IV from S. pneumoniae (cleaved form) 
    3KSB   Drug-free cleavage complex of topo IV from S. pneumoniae (resealed form) 
    3LTN   PD0305970-stabilised cleavage complex of topo IV from S. pneumoniae 
    3RAD    
    3RAE    
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MG
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    MG Mg
    MAGNESIUM ION
    PDQ
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    PDQ C18 H24 F N5 O2
    3-amino-7-{(3R)-3-[(1S)-1-aminoethyl]pyrrolidin- 1-yl}-1-cyclopropyl-6-fluoro-8-methylquinazoline- 2,4(1H,3H)-dione
    PDQ:3RAF
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:NA1061
     
 
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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