3TVB

A Highly Symmetric DNA G-4 Quadruplex/drug Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages.

Clark, G.R.Pytel, P.D.Squire, C.J.

(2012) Nucleic Acids Res 40: 5731-5738

  • DOI: 10.1093/nar/gks193
  • Primary Citation of Related Structures:  
    3TVB

  • PubMed Abstract: 
  • We have determined the X-ray structure of the complex between the DNA quadruplex d(5'-GGGG-3')(4) and daunomycin, as a potential model for studying drug-telomere interactions. The structure was solved at 1.08 Å by direct methods in space group I4. The asymmetric unit comprises a linear arrangement of one d(GGGG) strand, four daunomycin molecules, a second d(GGGG) strand facing in the opposite direction to the first, and Na and Mg cations ...

    We have determined the X-ray structure of the complex between the DNA quadruplex d(5'-GGGG-3')(4) and daunomycin, as a potential model for studying drug-telomere interactions. The structure was solved at 1.08 Å by direct methods in space group I4. The asymmetric unit comprises a linear arrangement of one d(GGGG) strand, four daunomycin molecules, a second d(GGGG) strand facing in the opposite direction to the first, and Na and Mg cations. The crystallographic 4-fold axis generates the biological unit, which is a 12-layered structure comprising two sets of four guanine layers, with four layers each of four daunomycins stacked between the 5' faces of the two quadruplexes. The daunomycin layers fall into two groups which are novel in their mode of self assembly. The only contacts between daunomycin molecules within any one of these layers are van der Waals interactions, however there is substantial π-π stacking between successive daunomycin layers and also with adjacent guanine layers. The structure differs significantly from all other parallel d(TGGGGT)(4) quadruplexes in that the 5' guanine adopts the unusual syn glycosyl linkage, refuting the widespread belief that such conformations should all be anti. In contrast to the related d(TGGGGT)/daunomycin complex, there are no ligand-quadruplex groove insertion interactions.


    Organizational Affiliation

    Chemistry Department and School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1044, New Zealand. g.clark@auckland.ac.nz



Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*GP*GP*G)-3')A, B 4N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DM1
Query on DM1

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B]
DAUNOMYCIN
C27 H29 N O10
STQGQHZAVUOBTE-VGBVRHCVSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
O [auth B],
P [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.209α = 90
b = 40.209β = 90
c = 49.831γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2012-07-11
    Changes: Database references
  • Version 1.2: 2020-01-29
    Changes: Advisory, Data collection, Derived calculations