4Z2E

Quinolone(Trovafloxacin)-DNA cleavage complex of gyrase from S. pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural studies of the drug-stabilized cleavage complexes of topoisomerase IV and gyrase from Streptococcus pneumoniae

Laponogov, I.Veselkov, D.A.Pan, X.-S.Selvarajah, J.Crevel, I.M.-T.Fisher, L.M.Sanderson, M.R.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit AA, C [auth B]499Streptococcus pneumoniaeMutation(s): 0 
Gene Names: gyrABM52_0349
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q8DPM2 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DPM2 
Go to UniProtKB:  Q8DPM2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit BB [auth C], D269Streptococcus pneumoniaeMutation(s): 0 
Gene Names: gyrBBM52_1967DJ38_04430
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0A4M0 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore P0A4M0 
Go to UniProtKB:  P0A4M0
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    Symmetrized E-site DNAE, H [auth G]15Escherichia coli
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      Symmetrized E-site DNAF, G [auth H]19Escherichia coli
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      TR6 (Subject of Investigation/LOI)
      Query on TR6

      Download Ideal Coordinates CCD File 
      I [auth F], K [auth H]Trovafloxacin
      C20 H15 F3 N4 O3
      WVPSKSLAZQPAKQ-CDMJZVDBSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      J [auth F], L [auth H]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.46 Å
      • R-Value Free: 0.292 
      • R-Value Work: 0.247 
      • R-Value Observed: 0.250 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 94.19α = 90
      b = 96.62β = 90
      c = 275.21γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      xia2data reduction
      xia2data scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Ligand Structure Quality Assessment  



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K010069/1

      Revision History  (Full details and data files)

      • Version 1.0: 2016-09-14
        Type: Initial release
      • Version 1.1: 2017-08-30
        Changes: Author supporting evidence, Derived calculations