2ET0 | pdb_00002et0

The structure of a three-way DNA junction in complex with a metallo-supramolecular helicate reveals a new target for drugs

PDB DOI: https://doi.org/10.2210/pdb2ET0/pdb
NAKB: 2ET0

Classification: DNA
Mutation(s): No

Deposited: 2005-10-27 Released: 2006-03-14
Deposition Author(s): Oleksi, A., Blanco, A.G., Boer, R., Uson, I., Aymami, J., Coll, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.291 (Depositor)
R-Value Work:
0.256 (Depositor), 0.260 (DCC)
R-Value Observed:
0.258 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Molecular Recognition of a Three-Way DNA Junction by a Metallosupramolecular Helicate

Oleksi, A., Blanco, A.G., Boer, R., Uson, I., Aymami, J., Rodger, A., Hannon, M.J., Coll, M.

(2006) Angew Chem Int Ed Engl 45: 1227-1231

PubMed: 16463312 Search on PubMed
DOI: https://doi.org/10.1002/anie.200503822
Primary Citation Related Structures:
2ET0

Organizational Affiliation

Institut de Biologia Molecular de Barcelona-CSIC and Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain.

Macromolecule Content

Total Structure Weight: 5.84 kDa
Atom Count: 435
Modeled Residue Count: 12
Deposited Residue Count: 12
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
5'-D(CPGPTPAPCPG)-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
NPM Query on NPM Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B]	G [auth A], H [auth A], I [auth A], J [auth A], M [auth B]	N-[(1E)-PYRIDIN-2-YLMETHYLENE]-N-[4-(4-{[(1E)-PYRIDIN-2-YLMETHYLENE]AMINO}BENZYL)PHENYL]AMINE C₂₅ H₂₀ N₄ OMZVNZJNZUGOJK-UOSOPFLXSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] K [auth B] C [auth A], D [auth A], E [auth A], F [auth A], K [auth B], L [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.291 (Depositor)
R-Value Work: 0.256 (Depositor), 0.260 (DCC)
R-Value Observed: 0.258 (Depositor)

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.2	α = 90
b = 71.2	β = 90
c = 71.2	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
XDS	data reduction
SHELXDE	phasing
SHELXL-97	refinement
XDS	data scaling
SHELXD	phasing
SHELXE	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-03-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-03-14
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations