1L1H

Crystal Structure of the Quadruplex DNA-Drug Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.139 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Structure of a G-quadruplex-Ligand Complex

Haider, S.M.Parkinson, G.N.Neidle, S.

(2003) J Mol Biol 326: 117-125

  • DOI: https://doi.org/10.1016/s0022-2836(02)01354-2
  • Primary Citation of Related Structures:  
    1L1H

  • PubMed Abstract: 

    Stabilisation of G-quadruplex structures formed from telomeric DNA, by means of quadruplex-selective ligands, is a means of inhibiting the telomerase enzyme from catalysing the synthesis of telomeric DNA repeats. In order to understand the molecular basis of ligand-quadruplex recognition, the crystal structure has been determined of such a complex, at 1.75A resolution. This complex is between a dimeric antiparallel G-quadruplex formed from the Oxytricha nova telomeric DNA sequence d(GGGGTTTTGGGG), and a di-substituted aminoalkylamido acridine compound. The structure shows that the acridine moiety is bound at one end of the stack of G-quartets, within one of the thymine loops. It is held in place by a combination of stacking interactions and specific hydrogen bonds with thymine bases. The stability of the ligand in this binding site has been confirmed by a 2ns molecular dynamics simulation.


  • Organizational Affiliation

    Cancer Research UK Biomolecular Structure Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, WC1N 1AX, London, UK.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'
A, B
12N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.139 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.451α = 90
b = 42.736β = 90
c = 26.926γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
SHELXL-97refinement

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PYNClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description