6Z1A

Ternary complex of Staphylococcus aureus DNA gyrase with AMK12 and DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report



Literature

Potent novel DNA gyrase inhibitors bind asymmetrically to their target using unforeseen symmetrical halogen bonds

Kolaric, A.Germe, T.Hrast, M.Stevenson, C.E.M.Lawson, D.M.Burton, N.Voros, J.Maxwell, A.Minovski, N.Anderluh, M.

To be published.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit B,DNA gyrase subunit ABD692Staphylococcus aureusMutation(s): 1 
Gene Names: gyrB
EC: 5.6.2.2
Find proteins for P20831 (Staphylococcus aureus)
Explore P20831 
Go to UniProtKB:  P20831
Find proteins for P0A0K8 (Staphylococcus aureus)
Explore P0A0K8 
Go to UniProtKB:  P0A0K8
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-3')E, F8Staphylococcus aureus subsp. aureus N315
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')G, H12Staphylococcus aureus subsp. aureus N315
      Small Molecules
      Ligands 5 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      Q52
      Query on Q52

      Download CCD File 
      G
      ~{N}-[(4-chlorophenyl)methyl]-1-[2-(6-methoxy-1,5-naphthyridin-4-yl)ethyl]piperidin-4-amine
      C23 H27 Cl N4 O
      MLGPJPYFHAIWJL-UHFFFAOYSA-N
       Ligand Interaction
      EPE
      Query on EPE

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      B, D
      4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
      C8 H18 N2 O4 S
      JKMHFZQWWAIEOD-UHFFFAOYSA-N
       Ligand Interaction
      DMS
      Query on DMS

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      D, E
      DIMETHYL SULFOXIDE
      C2 H6 O S
      IAZDPXIOMUYVGZ-UHFFFAOYSA-N
       Ligand Interaction
      MN
      Query on MN

      Download CCD File 
      B, D, G
      MANGANESE (II) ION
      Mn
      WAEMQWOKJMHJLA-UHFFFAOYSA-N
       Ligand Interaction
      CL
      Query on CL

      Download CCD File 
      D
      CHLORIDE ION
      Cl
      VEXZGXHMUGYJMC-UHFFFAOYSA-M
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.30 Å
      • R-Value Free: 0.217 
      • R-Value Work: 0.179 
      • R-Value Observed: 0.181 
      • Space Group: P 61
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 92.592α = 90
      b = 92.592β = 90
      c = 405.464γ = 120
      Software Package:
      Software NamePurpose
      REFMACrefinement
      Aimlessdata scaling
      PDB_EXTRACTdata extraction
      DIALSdata reduction
      REFMACphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      Slovenian Research AgencySloveniaP1-0017
      Slovenian Research AgencySloveniaP1-0208
      Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P012523/1
      Wellcome TrustUnited Kingdom110072/Z/15/Z

      Revision History 

      • Version 1.0: 2020-11-11
        Type: Initial release