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.

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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) 

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 
• DOI: https://doi.org/10.1002/anie.200503822
• Primary Citation of Related Structures:  
  2ET0

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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.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.84 kDa 
• Atom Count: 435 
• Modelled 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*TP*AP*CP*G)-3'	A, B	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NPM	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
FE2	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

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

Entry History 

Deposition Data

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

Revision History  

• 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