1Z3F

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.242
R-Value Work: 0.220
R-Value Observed: 0.222

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1107/S0907444905015404
Primary Citation of 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.

Organizational Affiliation

Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Parc Científic de Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain. acpcri@ibmb.csic.es

Macromolecule Content

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

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(CPGPAPTPCPG)-3'	A, B	6	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EL Query on EL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	ELLIPTICINE C₁₇ H₁₅ N₂ CTSPAMFJBXKSOY-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	D [auth A], F [auth B], G [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.242
R-Value Work: 0.220
R-Value Observed: 0.222
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-07-19

Deposition Author(s):

Revision History (Full details and data files)

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