1VS2

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

• PDB DOI: https://doi.org/10.2210/pdb1VS2/pdb
• NAKB: 1VS2

• Classification: DNA/ANTIBIOTIC
• Organism(s): Streptomyces sp.
• Mutation(s): No 


• Deposited: 1986-10-21 Released: 2006-06-27 
• Deposition Author(s): Wang, A.H.-J., Ughetto, G., Quigley, G.J., Rich, A.

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Experimental Data Snapshot

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

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

• PubMed: 3271447 
• 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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 3.57 kDa 
• Atom Count: 237 
• Modelled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TRIOSTIN A	B	8	Streptomyces sp.	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'	A	8	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QUI	C [auth B], D [auth B]	2-CARBOXYQUINOXALINE C9 H6 N2 O2 UPUZGXILYFKSGE-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MVA	B	L-PEPTIDE LINKING	C6 H13 N O2		VAL

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000488	B	TRIOSTIN A	Cyclic depsipeptide / Anticancer

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 = 40.9	α = 90
b = 40.9	β = 90
c = 80.7	γ = 120

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-27 
Deposition Author(s): Wang, A.H.-J., Ughetto, G., Quigley, G.J., Rich, A.

Revision History  

• 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
• Version 1.6: 2023-12-27
  Changes: Advisory, Data collection, Database references, Derived calculations