159D

SIDE BY SIDE BINDING OF TWO DISTAMYCIN A DRUGS IN THE MINOR GROOVE OF AN ALTERNATING B-DNA DUPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex.

Chen, X.Ramakrishnan, B.Rao, S.T.Sundaralingam, M.

(1994) Nat.Struct.Mol.Biol. 1: 169-175


  • PubMed Abstract: 
  • Here we report the 1.8A X-ray structure of a 2:1 drug-DNA complex between distamycin A and an alternating B-DNA octamer duplex d(ICICICIC)2. The two distamycin A molecules are bound side by side with dyad symmetry in an antiparallel orientation in th ...

    Here we report the 1.8A X-ray structure of a 2:1 drug-DNA complex between distamycin A and an alternating B-DNA octamer duplex d(ICICICIC)2. The two distamycin A molecules are bound side by side with dyad symmetry in an antiparallel orientation in the expanded minor groove. The amides of each drug molecule are hydrogen bonded to the minor groove base atoms of only one DNA strand. The complex not only shows binding of two drug molecules, but the DNA duplex also exhibits striking low-high alternations in the helical twist angles, the sugar puckering and the phosphate conformations, providing the basis for a new model for an alternating B-DNA with a dinucleotide repeat.


    Organizational Affiliation

    Department of Chemistry, Ohio State University, Columbus 43210, USA.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*IP*CP*IP*CP*IP*CP*IP*C)-3')A8N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DMY
Query on DMY

Download SDF File 
Download CCD File 
A
DISTAMYCIN A
DISTAMYCIN; STALLIMYCIN
C22 H27 N9 O4
UPBAOYRENQEPJO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.150 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 27.930α = 90.00
b = 27.930β = 90.00
c = 57.670γ = 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: 1995-02-07
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance