1Z3F | pdb_00001z3f

Structure of ellipticine in complex with a 6-bp DNA

• PDB DOI: https://doi.org/10.2210/pdb1Z3F/pdb
• NAKB: 1Z3F

• Classification: DNA
• Mutation(s): No 


• Deposited: 2005-03-12 Released: 2005-07-19 
• Deposition Author(s): Canals, A., Purciolas, M., Aymami, J., Coll, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.242 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

The anticancer agent ellipticine unwinds DNA by intercalative binding in an orientation parallel to base pairs.

Canals, A., Purciolas, M., Aymami, J., Coll, M.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1009-1012

• PubMed: 15983425 
• DOI: https://doi.org/10.1107/S0907444905015404
• Primary Citation Related Structures: 
  1Z3F


• PubMed Abstract: 
  

  Ellipticine is a natural plant product that has been found to be a powerful anticancer drug. Although still unclear, its mechanism of action is considered to be mainly based on DNA intercalation and/or the inhibition of topoisomerase II. Many experimental data suggest an intercalation based on stacking interactions along the major base-pair axis, but alternative binding modes have been proposed, in particular for ellipticine derivatives. The 1.5 A resolution structure of ellipticine complexed to a 6 bp oligonucleotide unveils its mode of binding and enables a detailed analysis of the distorting effects of the drug on the DNA.

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Organizational Affiliation: 
• Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.29 kDa 
• Atom Count: 308 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*AP*TP*CP*G)-3'	A, B	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EL	C [auth A], E [auth B]	ELLIPTICINE C17 H15 N2 CTSPAMFJBXKSOY-UHFFFAOYSA-O
CO	D [auth A], F [auth B], G [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.242 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.86	α = 90
b = 24.86	β = 90
c = 78.86	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-19 
Deposition Author(s): Canals, A., Purciolas, M., Aymami, J., Coll, M.

Revision History  

• Version 1.0: 2005-07-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations