4Z2C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

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)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DPM2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit BB [auth C],
D
269Streptococcus 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A4M0
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsLengthOrganismImage
Symmetrized E-site DNAE,
H [auth G]
15Escherichia coli
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChainsLengthOrganismImage
Symmetrized E-site DNAF,
G [auth H]
19Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MFX
Query on MFX

Download Ideal Coordinates CCD File 
I [auth F],
J [auth H]
1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
C21 H24 F N3 O4
FABPRXSRWADJSP-MEDUHNTESA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.03α = 90
b = 94.95β = 90
c = 274.29γ = 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