3RAD

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

Structural Biology Knowledgebase: 3RAD SBKB.org


Experimental Data Snapshot

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

Literature

Macromolecules
Sequence Display for 3RAD

Classification: ISOMERASE / DNA / ANTIBIOTIC

Total Structure Weight: 185562.75


Macromolecule Entities
Molecule Chains Length Organism Details
DNA topoisomerase 4 subunit A A, B 496 Streptococcus pneumoniae EC#: 5.99.1.3 IUBMB
Fragment: UNP residues 1-488
Mutation: I257T
Gene Name(s): parC SP_0855
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA topoisomerase 4 subunit B C, D 268 Streptococcus pneumoniae EC#: 5.99.1.3 IUBMB
Fragment: UNP residues 404-647
Mutation: V460I, T644A
Gene Name(s): parE SP_0852
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*CP*AP*TP*GP*AP*AP*T)-3' E 7 synthetic
5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*G)-3' F 11 synthetic
5'-D(*CP*GP*TP*GP*CP*AP*T)-3' G 7 synthetic
5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*G)-3' H 11 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NFX
Query on NFX

F, H 7-[(3R)-3-aminopyrrolidin-1-yl]-8-chloro- 1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinoline- 3-carboxylic acid
Clinafloxacin (Synonym)
C17 H17 Cl F N3 O3
QGPKADBNRMWEQR-MRVPVSSYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

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
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 157.13 α = 90.00
b = 157.13 β = 90.00
c = 211.09 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-28
  • Released Date: 2012-04-25
  • Deposition author(s): Laponogov, I., Pan, X.-S., Veselkov, D.A., McAuley, K.E., Fisher, L.M., Sanderson, M.R.

Revision History

No revisions since initial release