1R68 | pdb_00001r68

Role of the amino sugar in DNA binding of disaccharide anthracyclines: crystal structure of MAR70/d(CGATCG) complex

• PDB DOI: https://doi.org/10.2210/pdb1R68/pdb
• NAKB: 1R68

• Classification: DNA
• Mutation(s): No 


• Deposited: 2003-10-15 Released: 2005-02-22 
• Deposition Author(s): Temperini, C., Cirilli, M., Aschi, M., Ughetto, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.450 (DCC) 
• R-Value Work: 
  0.460 (DCC) 

Literature

Role of the amino sugar in DNA binding of disaccharide anthracyclines: crystal structure of the complex MAR70/d(CGATCG).

Temperini, C., Cirilli, M., Aschi, M., Ughetto, G.

(2005) Bioorg Med Chem 13: 1673-1679

• PubMed: 15698785 
• DOI: https://doi.org/10.1016/j.bmc.2004.12.007
• Primary Citation of Related Structures:  
  1R68


• PubMed Abstract: 
  

  Disaccharide anthracyclines analogues have been shown to exhibit different antitumour activity as compared with parents compounds doxorubicin and daunomycin. Here we report the crystal structure of the disaccharide analog MAR70 complexed with the DNA hexamer d(CGATCG). The structure has been solved at 1.54A resolution and is similar to previous crystallized anthracycline-DNA complexes with both sugar rings of the disaccharide chain lying in the DNA minor groove. Comparison with the structure of MEN10755 another disaccharide anthracycline co-crystallized with the same DNA hexamer suggests a correlation between the position of the amino sugar on the disaccharide chain and the conformation of this moiety when binding to DNA. This is discussed with respect to the influence on drug activity and on the possible interaction with other cellular targets.

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Organizational Affiliation: 
• Department of Chemistry, University of Florence, 50019 Sesto F.no (FI), Italy.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.47 kDa 
• Atom Count: 188 
• Modeled Residue Count: 6 
• Deposited Residue Count: 6 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAR	B [auth A]	4'-EPI-4'-(2-DEOXYFUCOSE)DAUNOMYCIN C33 H39 N O13 QTGKDZKONUUXOU-NIGIIATCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.450 (DCC) 
• R-Value Work:  0.460 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.19	α = 90
b = 28.19	β = 90
c = 53.25	γ = 90

Software Package:

Software Name	Purpose
TEXAN	data collection
TEXAN	data reduction
AMoRE	phasing
SHELXL-97	refinement
TEXSAN	data reduction
TEXSAN	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-22 
Deposition Author(s): Temperini, C., Cirilli, M., Aschi, M., Ughetto, G.

Revision History  

• Version 1.0: 2005-02-22
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Structure summary