3EY0

A new form of DNA-drug interaction in the minor groove of a coiled coil

• PDB DOI: https://doi.org/10.2210/pdb3EY0/pdb
• NAKB: 3EY0

• Classification: DNA
• Mutation(s): No 


• Deposited: 2008-10-17 Released: 2009-10-27 
• Deposition Author(s): Pous, J., Moreno, T., Subirana, J.A., Campos, J.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.277 
• R-Value Work: 0.216 
• R-Value Observed: 0.222 

Starting Model: in silico

Literature

Coiled-coil conformation of a pentamidine-DNA complex

Moreno, T., Pous, J., Subirana, J.A., Campos, J.L.

(2010) Acta Crystallogr D Biol Crystallogr 66: 251-257

• PubMed: 20179336 
• DOI: https://doi.org/10.1107/S0907444909055693
• Primary Citation of Related Structures:  
  3EY0


• PubMed Abstract: 
  

  The coiled-coil structure formed by the complex of the DNA duplex d(ATATATATAT)(2) with pentamidine is presented. The duplex was found to have a mixed structure containing Watson-Crick and Hoogsteen base pairs. The drug stabilizes the coiled coil through the formation of cross-links between neighbouring duplexes. The central part of the drug is found in the minor groove as expected, whereas the charged terminal amidine groups protrude and interact with phosphates from neighbouring molecules. The formation of cross-links may be related to the biological effects of pentamidine, which is used as an antiprotozoal agent in trypanosomiasis, leishmaniasis and pneumonias associated with AIDS. The DNA sequence that was used is highly abundant in most eukaryotic genomes. However, very few data are available on DNA sequences which only contain A.T base pairs.

---

Organizational Affiliation: 

Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, E-08028 Barcelona, Spain.

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 6.45 kDa 
• Atom Count: 481 
• Modelled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DTP*DAP*DT)-3'	A, B	10	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PNT	C [auth A]	1,5-BIS(4-AMIDINOPHENOXY)PENTANE C19 H24 N4 O2 XDRYMKDFEDOLFX-UHFFFAOYSA-N
MG	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.277 
• R-Value Work: 0.216 
• R-Value Observed: 0.222 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.789	α = 90
b = 27.789	β = 90
c = 311.95	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Pous, J., Moreno, T., Subirana, J.A., Campos, J.L.

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-04-03
  Changes: Refinement description