3EUM

A bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine BSU-6066

• PDB DOI: https://doi.org/10.2210/pdb3EUM/pdb
• NAKB: 3EUM

• Classification: DNA
• Mutation(s): No 


• Deposited: 2008-10-10 Released: 2008-10-21 
• Deposition Author(s): Campbell, N.H., Parkinson, G., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.270 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 

Literature

Selectivity in Ligand Recognition of G-Quadruplex Loops.

Campbell, N.H., Patel, M., Tofa, A.B., Ghosh, R., Parkinson, G.N., Neidle, S.

(2009) Biochemistry 48: 1675-1680

• PubMed: 19173611 
• DOI: https://doi.org/10.1021/bi802233v
• Primary Citation of Related Structures:  
  3EM2, 3EQW, 3ERU, 3ES0, 3ET8, 3EUI, 3EUM


• PubMed Abstract: 
  

  A series of disubstituted acridine ligands have been cocrystallized with a bimolecular DNA G-quadruplex. The ligands have a range of cyclic amino end groups of varying size. The crystal structures show that the diagonal loop in this quadruplex results in a large cavity for these groups, in contrast to the steric constraints imposed by propeller loops in human telomeric quadruplexes. We conclude that the nature of the loop has a significant influence on ligand selectivity for particular quadruplex folds.

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Organizational Affiliation: 

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

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 8.28 kDa 
• Atom Count: 600 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*DGP*DGP*DGP*DGP*DTP*DTP*DTP*DTP*DGP*DGP*DGP*DG)-3'	A, B	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCQ	F [auth A]	3,6-Bis[3-(azepan-1-yl)propionamido]acridine C31 H41 N5 O2 MSWYQCALXGGGBX-UHFFFAOYSA-N
K	C [auth A], D [auth A], E [auth A], G [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.270 
• R-Value Work: 0.222 
• R-Value Observed: 0.224 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.62	α = 90
b = 42.307	β = 90
c = 27.079	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
PHASER	phasing
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-21 
Deposition Author(s): Campbell, N.H., Parkinson, G., Neidle, S.

Revision History  

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description