121D

MOLECULAR STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor groove binding drug netropsin.

Tabernero, L.Verdaguer, N.Coll, M.Fita, I.van der Marel, G.A.van Boom, J.H.Rich, A.Aymami, J.

(1993) Biochemistry 32: 8403-8410


  • PubMed Abstract: 
  • The molecular structure of the complex between the minor groove binding drug netropsin and the dodecamer d(CGCAAATTTGCG) has been solved and refined by X-ray diffraction analysis to an R-factor of 19.8% and 2.2-A resolution. The drug lies in the narr ...

    The molecular structure of the complex between the minor groove binding drug netropsin and the dodecamer d(CGCAAATTTGCG) has been solved and refined by X-ray diffraction analysis to an R-factor of 19.8% and 2.2-A resolution. The drug lies in the narrow minor groove of the B-DNA fragment, covering five of the six A.T base pairs (from A5.T20 to T9.A16). The long six A.T base pair tract allows the drug to bind in a position that optimizes its contacts with the DNA, establishing hydrogen bonds with O2 of thymines and N3 of adenines. The DNA molecule shows a high propeller twist only at the A6.T19 step of the A-tract. Two three-centered hydrogen bonds are observed in the major groove at half of the A-tract.


    Organizational Affiliation

    Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')A,B12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NT
Query on NT

Download SDF File 
Download CCD File 
A
NETROPSIN
C18 H26 N10 O3
IDBIFFKSXLYUOT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 25.650α = 90.00
b = 42.030β = 90.00
c = 65.330γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance