4KPE

Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones.

Laponogov, I.Pan, X.S.Veselkov, D.A.Cirz, R.T.Wagman, A.Moser, H.E.Fisher, L.M.Sanderson, M.R.

(2016) Open Biol 6: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase 4 subunit A
A, B
496Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Mutation(s): 1 
Gene Names: parC
EC: 5.99.1.3
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  P72525
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase 4 subunit B
C, D
268Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Mutation(s): 2 
Gene Names: parE
EC: 5.99.1.3
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  Q59961
Entity ID: 3
MoleculeChainsLengthOrganism
E-site DNA1E7synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
E-site DNA2F11synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
E-site DNA3G7synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
E-site DNA4H11synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AF5
Query on AF5

Download SDF File 
Download CCD File 
F, H
(7aR,8R)-8-amino-4-cyclopropyl-12-fluoro-1-oxo-4,7,7a,8,9,10-hexahydro-1H-pyrrolo[1',2':1,7]azepino[2,3-h]quinoline-2-carboxylic acid
C20 H20 F N3 O3
KZNQXATUOHSRHR-HZPDHXFCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.154 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 157.830α = 90.00
b = 157.830β = 90.00
c = 210.710γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
GDEdata collection
PHENIXrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2018-10-03
    Type: Data collection, Database references, Source and taxonomy