1VS2

Interactions of quinoxaline antibiotic and DNA: the molecular structure of a TRIOSTIN A-D(GCGTACGC) complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.200 

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This is version 1.5 of the entry. See complete history. 


Literature

Interactions of Quinoxaline Antibiotic and DNA: The Molecular Structure of a Triostin A-D(Gcgtacgc) Complex.

Wang, A.H., Ughetto, G., Quigley, G.J., Rich, A.

(1986) J Biomol Struct Dyn 4: 319

  • DOI: https://doi.org/10.1080/07391102.1986.10506353
  • Primary Citation of Related Structures:  
    1VS2

  • PubMed Abstract: 

    • The crystal structure of a DNA octamer d(GCGTACGC) complexed to an antitumor antibiotic, triostin A, has been solved and refined to 2.2 A resolution by x-ray diffraction analysis. The antibiotic molecule acts as a true bis intercalator surrounding the d(CpG) sequence at either end of the unwound right-handed DNA double helix ...

    The crystal structure of a DNA octamer d(GCGTACGC) complexed to an antitumor antibiotic, triostin A, has been solved and refined to 2.2 A resolution by x-ray diffraction analysis. The antibiotic molecule acts as a true bis intercalator surrounding the d(CpG) sequence at either end of the unwound right-handed DNA double helix. As previously observed in the structure of triostin A-d(CGTACG) complex (A.H.-J. Wang, et. al., Science, 225, 1115-1121 (1984)), the alanine amino acid residues of the drug molecule form sequence-specific hydrogen bonds to guanines in the minor groove. The two central A.T base pairs are in Hoogsteen configuration with adenine in the syn conformation. In addition, the two terminal G.C base pairs flanking the quinoxaline rings are also held together by Hoogsteen base pairing. This is the first observation in an oligonucleotide of. Hoogsteen G.C base pairs where the cytosine is protonated. The principal functional components of a bis-intercalative compound are discussed.

    Related Citations: 
    • Non-Watson-Crick G-C and A-T Base Pairs in a DNA-Antibiotic Complex
      Quigley, G.J., Ughetto, G., Van Der Marel, G.A., Van Boom, J.H., Wang, A.H.-J., Rich, A.
      (1986) Science 232: 1255
    Organizational Affiliation: 

    Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TRIOSTIN AB8Streptomyces sp.Mutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'A8N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QUI
Query on QUI
Download Ideal Coordinates CCD File 
C [auth B],
D [auth B]		2-CARBOXYQUINOXALINE
C9 H6 N2 O2
UPUZGXILYFKSGE-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MVA
Query on MVA		B L-PEPTIDE LINKINGC6 H13 N O2VAL
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000488
Query on PRD_000488		BTRIOSTIN ACyclic depsipeptide / Anticancer Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.200 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.9α = 90
b = 40.9β = 90
c = 80.7γ = 120
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-27
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-02-08
    Changes: Derived calculations
  • Version 1.5: 2013-02-27
    Changes: Other