5HIX

Cocrystal structure of an anti-parallel DNA G-quadruplex and a tetra-Quinoline Foldamer

• PDB DOI: https://doi.org/10.2210/pdb5HIX/pdb
• NAKB: 5HIX

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2016-01-12 Released: 2016-11-02 
• Deposition Author(s): Mandal, P.K., Baptiste, B., Langlois d'Estaintot, B., Kauffmann, B., Huc, I.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.288 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Multivalent Interactions between an Aromatic Helical Foldamer and a DNA G-Quadruplex in the Solid State.

Mandal, P.K., Baptiste, B., Langlois d'Estaintot, B., Kauffmann, B., Huc, I.

(2016) Chembiochem 17: 1911-1914

• PubMed: 27472456 
• DOI: https://doi.org/10.1002/cbic.201600281
• Primary Citation of Related Structures:  
  5HIX


• PubMed Abstract: 
  

  Quinoline-based oligoamide foldamers have been identified as a potent class of ligands for G-quadruplex DNA. Their helical structure is thought to target G-quadruplex loops or grooves and not G-tetrads. We report a co-crystal structure of the antiparallel hairpin dimeric DNA G-quadruplex (G ₄ T ₄ G ₄ ) ₂ with tetramer 1-a helically folded oligo-quinolinecarboxamide bearing cationic side chains-that is consistent with this hypothesis. Multivalent foldamer-DNA interactions that modify the packing of (G ₄ T ₄ G ₄ ) ₂ in the solid state are observed.

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Organizational Affiliation: 

University of Bordeaux, CBMN, UMR 5248), Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 8.79 kDa 
• Atom Count: 595 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Dimeric G-quadruplex	A, B	12	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
61Q	G [auth A]	4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-nitroquinolin-2-yl]carbonyl}amino)quinolin-2-yl]carbonyl}amino)quinolin-2-yl]carbonyl}amino)quinoline-2-carboxylic acid C52 H52 N12 O11 PDPDTUNURBJNEI-UHFFFAOYSA-N
K	C [auth A], D [auth A], E [auth A], F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.288 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.701	α = 90
b = 31.701	β = 90
c = 97.373	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
AMoRE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Mandal, P.K., Baptiste, B., Langlois d'Estaintot, B., Kauffmann, B., Huc, I.

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Funding Organization	Location	Grant Number
European Research Council	France	ERC-2012-AdG-320892

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description