3K9F

Detailed structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases

Structural Biology Knowledgebase: 3K9F SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.183

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3K9F

Classification: ISOMERASE / DNA

Total Structure Weight: 195341.09


Macromolecule Entities
Molecule Chains Length Organism Details
DNA topoisomerase 4 subunit A A, B 496 Streptococcus pneumoniae EC#: 5.99.1.3 IUBMB
Fragment: residues 1-488
Gene Name(s): parC SP_0855
DNA topoisomerase 4 subunit B C, D 268 Streptococcus pneumoniae EC#: 5.99.1.3 IUBMB
Fragment: residues 404-647
Gene Name(s): parE SP_0852
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*AP*CP*CP*AP*AP*GP*GP*T*CP*AP*TP*GP*AP*AP*T)-3') E 15 synthetic DNA E site
DNA (5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3') F 19 synthetic DNA E site
DNA (5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*T)-3') G 15 synthetic DNA E site
DNA (5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3') H 19 synthetic DNA E site

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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.183
  • Space Group: P 32

Unit Cell:

Length (Å) Angle (°)
a = 122.41 α = 90.00
b = 122.41 β = 90.00
c = 178.29 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-10-15
  • Released Date: 2009-10-27
  • Deposition author(s): Laponogov, I., Pan, X.-S., Veselkov, D.A., Fisher, L.M., Sanderson, M.R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4