4JIY

RNA three-way junction stabilized by a supramolecular di-iron(II) cylinder drug


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Binding of a designed anti-cancer drug to the central cavity of an RNA three-way junction.

Phongtongpasuk, S.Paulus, S.Schnabl, J.Sigel, R.K.Spingler, B.Hannon, M.J.Freisinger, E.

(2013) Angew.Chem.Int.Ed.Engl. 52: 11513-11516

  • DOI: 10.1002/anie.201305079

  • PubMed Abstract: 
  • Getting to the heart of it: Co-crystallization of an RNA three-way junction with a cylindrical di-iron(II)-based anti-cancer drug (green) results in π-stacking interactions between the cylinder and the central base pairs of the RNA structure. The sha ...

    Getting to the heart of it: Co-crystallization of an RNA three-way junction with a cylindrical di-iron(II)-based anti-cancer drug (green) results in π-stacking interactions between the cylinder and the central base pairs of the RNA structure. The shape, size, and cationic nature of the cylinder were found to be responsible for this perfect fit. Native gel electrophoresis studies confirmed stabilization of the RNA three-way junction by the iron(II) cylinder.


    Organizational Affiliation

    Institut für Anorganische Chemie, Universität Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland) http://www.chem.uzh.ch; School of Chemistry, University of Birmingham, Edgbaston, Birmingham B152TT (UK).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-(CGUACG)-3'A6N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPM
Query on NPM

Download SDF File 
Download CCD File 
A
N-[(1E)-PYRIDIN-2-YLMETHYLENE]-N-[4-(4-{[(1E)-PYRIDIN-2-YLMETHYLENE]AMINO}BENZYL)PHENYL]AMINE
1,1-BIS(N-(4-PHENYL)-2-PYRIDYLCARBOXALDIMINE)METHANE
C25 H20 N4
OMZVNZJNZUGOJK-UOSOPFLXSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.224 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 45.745α = 90.00
b = 45.745β = 90.00
c = 45.745γ = 90.00
Software Package:
Software NamePurpose
XPREPdata reduction
SHELXDphasing
XDSdata reduction
SHELXL-97refinement
RemDAqdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-10-02
    Type: Database references
  • Version 1.2: 2013-11-06
    Type: Database references