1VS2 | pdb_00001vs2

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 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

PubMed: 3271447 Search on PubMed
DOI: https://doi.org/10.1080/07391102.1986.10506353
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by: Sequence | 3D Structure

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

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
5'-D(GPCPGPTPAPCPGPC)-3'	A	8	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QUI Query on QUI Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B]	C [auth B], D [auth B]	2-CARBOXYQUINOXALINE C₉ H₆ N₂ O₂ UPUZGXILYFKSGE-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DSN Query on DSN	B	D-PEPTIDE LINKING	C₃ H₇ N O₃		--
MVA Query on MVA	B	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
NCY Query on 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 Query on PRD_000488	B	TRIOSTIN A	Cyclic depsipeptide / Anticancer		Interactions Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Observed: 0.200 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2006-06-27

Deposition Author(s):

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