3GDD | pdb_00003gdd

An inverted anthraquinone-DNA crystal structure

• PDB DOI: https://doi.org/10.2210/pdb3GDD/pdb
• NAKB: 3GDD

• Classification: DNA
• Mutation(s): No 


• Deposited: 2009-02-24 Released: 2010-03-09 
• Deposition Author(s): Subirana, J.A., De Luchi, D., Wright, G., Gouyette, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.259 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Structure of a stacked anthraquinone-DNA complex

De Luchi, D., Uson, I., Wright, G., Gouyette, C., Subirana, J.A.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1019-1022

• PubMed: 20823516 
• DOI: https://doi.org/10.1107/S1744309110030034
• Primary Citation Related Structures: 
  3GDD


• PubMed Abstract: 
  

  The crystal structure of the telomeric sequence d(UBrAGG) interacting with an anthraquinone derivative has been solved by MAD. In all previously studied complexes of intercalating drugs, the drug is usually sandwiched between two DNA base pairs. Instead, the present structure looks like a crystal of stacked anthraquinone molecules in which isolated base pairs are intercalated. Unusual base pairs are present in the structure, such as G.G and A.UBr reverse Watson-Crick base pairs.

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Organizational Affiliation: 
• Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.25 kDa 
• Atom Count: 259 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*(BRU)P*AP*GP*G)-3'	A, B	4	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5BD	D [auth A], E [auth A], F [auth A], G [auth B]	N,N'-(9,10-dioxo-9,10-dihydroanthracene-2,7-diyl)bis[2-(dimethylamino)acetamide] C22 H24 N4 O4 BQUQDCVNESTXAU-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.259 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.698	α = 90
b = 29.698	β = 90
c = 60.883	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Subirana, J.A., De Luchi, D., Wright, G., Gouyette, C.

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations