3RAF

Quinazolinedione-DNA cleavage complex of type IV topoisomerase from S. pneumoniae

Structural Biology Knowledgebase: 3RAF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.167

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3RAF

Classification: ISOMERASE / DNA / ANTIBIOTIC

Total Structure Weight: 185505.42


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
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
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
PDQ
Query on PDQ

F, H 3-amino-7-{(3R)-3-[(1S)-1-aminoethyl]pyrrolidin- 1-yl}-1-cyclopropyl-6-fluoro-8-methylquinazoline- 2,4(1H,3H)-dione
C18 H24 F N5 O2
SMONLCFJGCJROJ-WDEREUQCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, 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: 3.24 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.167
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 158.55 α = 90.00
b = 158.55 β = 90.00
c = 210.33 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-03-28
  • Released Date: 2012-03-28
  • 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