1VTG | pdb_00001vtg

THE MOLECULAR STRUCTURE OF A DNA-TRIOSTIN A COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1VTG/pdb
• NAKB: 1VTG

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


• Deposited: 1988-08-18 Released: 2011-07-13 
• Deposition Author(s): Wang, A.H.-J., Ughetto, G., Quigley, G.J., Hakoshima, T., Van Der Marel, G.A., Van Boom, J.H., Rich, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Observed: 
  0.189 (Depositor) 

Literature

The molecular structure of a DNA-triostin A complex.

Wang, A.H., Ughetto, G., Quigley, G.J., Hakoshima, T., van der Marel, G.A., van Boom, J.H., Rich, A.

(1984) Science 225: 1115-1121

• PubMed: 6474168 
• DOI: https://doi.org/10.1126/science.6474168
• Primary Citation Related Structures: 
  1VTG


• PubMed Abstract: 
  

  The molecular structure of triostin A, a cyclic octadepsipeptide antibiotic, has been solved complexed to a DNA double helical fragment with the sequence CGTACG (C, cytosine; G, guanine; T, thymine; A, adenine). The two planar quinoxaline rings of triostin A bis intercalate on the minor groove of the DNA double helix surrounding the CG base pairs at either end. The alanine residues form hydrogen bonds to the guanines. Base stacking in the DNA is perturbed, and the major binding interaction involves a large number of van der Waals contacts between the peptides and the nucleic acid. The adenine residues in the center are in the syn conformation and are paired to thymine through Hoogsteen base pairing.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.95 kDa 
• Atom Count: 196 
• Modeled Residue Count: 14 
• Deposited Residue Count: 14 
• 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
DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')	A	6	synthetic construct

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
DSN	B	D-PEPTIDE LINKING	C3 H7 N O3		--
MVA	B	L-PEPTIDE LINKING	C6 H13 N O2		VAL
NCY	B	L-PEPTIDE LINKING	C4 H9 N O2 S		--

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: 1.67 Å
• R-Value Observed: 0.189 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.35	α = 90
b = 62.38	β = 90
c = 61.26	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Wang, A.H.-J., Ughetto, G., Quigley, G.J., Hakoshima, T., Van Der Marel, G.A., Van Boom, J.H., Rich, A.

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2011-10-05
  Changes: Derived calculations, Structure summary
• Version 1.2: 2012-02-22
  Changes: Structure summary
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2018-10-10
  Changes: Advisory, Data collection, Database references, Source and taxonomy
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references, Derived calculations