3RAE

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

Structural Biology Knowledgebase: 3RAE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.186

Literature

Macromolecules
Sequence Display for 3RAE

Classification: ISOMERASE / DNA / ANTIBIOTIC

Total Structure Weight: 185553.91


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
LFX
Query on LFX

F, H (3S)-9-fluoro-3-methyl-10-(4-methylpiperazin- 1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4- ij]quinoline-6-carboxylic acid
Levofloxacin (Synonym)
C18 H20 F N3 O4
GSDSWSVVBLHKDQ-JTQLQIEISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D, G 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: 2.9 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.186
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 157.83 α = 90.00
b = 157.83 β = 90.00
c = 211.15 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

  • 2016-04-20
    Type: Citation | Details: Citation update