3NX5

The crystal structure of Sanguinarine bound to DNA d(CGTACG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-Ray diffraction analyses of the natural isoquinoline alkaloids Berberine and Sanguinarine complexed with double helix DNA d(CGTACG)

Ferraroni, M.Bazzicalupi, C.Bilia, A.R.Gratteri, P.

(2011) Chem.Commun.(Camb.) 47: 4917-4919

  • DOI: 10.1039/c1cc10971e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The first crystal structures of Berberine and Sanguinarine intercalated with a d(CGTACG)(2) DNA sequence were obtained by X-ray diffraction analysis at 2.3 Å resolution. Both drugs join the end of two "two-molecules" DNA units, stacked in a non-class ...

    The first crystal structures of Berberine and Sanguinarine intercalated with a d(CGTACG)(2) DNA sequence were obtained by X-ray diffraction analysis at 2.3 Å resolution. Both drugs join the end of two "two-molecules" DNA units, stacked in a non-classic intercalation site formed by six bases. Sanguinarine interacts with d(CGTACG)(2) DNA in its iminium form.


    Organizational Affiliation

    Department of Chemistry Ugo Schiff, University of Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Firenze, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*TP*AP*CP*G)-3'A,B,C,D6N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
SAU
Query on SAU

Download SDF File 
Download CCD File 
C
13-methyl[1,3]benzodioxolo[5,6-c][1,3]dioxolo[4,5-i]phenanthridin-13-ium
Sanguinarine
C20 H14 N O4
INVGWHRKADIJHF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.252 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 29.992α = 90.00
b = 29.992β = 90.00
c = 119.069γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
MOLREPphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance