3RAD

Quinolone(Clinafloxacin)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Inhibitor-stabilised cleavage complexes of topoisomerase IIa: structural analysis of drug-dependent inter- and intramolecular interactions

Laponogov, I.Pan, X.-S.Veselkov, D.A.McAuley, K.E.Fisher, L.M.Sanderson, M.R.

To be published.

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)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)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
5'-D(*CP*AP*TP*GP*AP*AP*T)-3'E7N/A
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*G)-3'F11N/A
Entity ID: 5
MoleculeChainsLengthOrganism
5'-D(*CP*GP*TP*GP*CP*AP*T)-3'G7N/A
Entity ID: 6
MoleculeChainsLengthOrganism
5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*G)-3'H11N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NFX
Query on NFX

Download SDF File 
Download CCD File 
F, H
7-[(3R)-3-aminopyrrolidin-1-yl]-8-chloro-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
Clinafloxacin
C17 H17 Cl F N3 O3
QGPKADBNRMWEQR-MRVPVSSYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.177 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 157.128α = 90.00
b = 157.128β = 90.00
c = 211.091γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
GDEdata collection
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-25
    Type: Initial release