4KPF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 

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
ParC55
A, B
496Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Mutation(s): 0 
Gene Names: parC
EC: 5.6.2.3
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  P72525
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ParE30
C, D
268Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Mutation(s): 0 
Gene Names: parE
EC: 5.6.2.3
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  Q59961
Entity ID: 3
MoleculeChainsLengthOrganism
E-site1E7synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
E-site2F11synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
E-site3G7synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
E-site4H11synthetic 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, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
1UV
Query on 1UV

Download SDF File 
Download CCD File 
H
(3aS,4R)-4-amino-13-cyclopropyl-8-fluoro-10-oxo-3a,4,5,6,10,13-hexahydro-1H,3H-pyrrolo[2',1':3,4][1,4]oxazepino[5,6-h]quinoline-11-carboxylic acid
C19 H20 F N3 O4
DXDXKLSOWWPCNV-HUUCEWRRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 157.860α = 90.00
b = 157.860β = 90.00
c = 210.780γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
GDEdata collection
XDSdata reduction
PHASERphasing
XSCALEdata scaling

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