308D

BINDING OF DAUNOMYCIN TO B-D-GLUCOSYLATED DNA FOUND IN PROTOZOA TRYPANOSOMA BRUCEI STUDIED BY X-RAY CRYSTALLOGRAPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Binding of Daunomycin to beta-D-Glucosylated DNA Found in Protozoa Trypanosoma brucei Studied by X-Ray Crystallography

Gao, Y.-G.Robinson, H.Wijsman, E.R.Van Der Marel, G.A.Van Boom, J.H.Wang, A.H.-J.

(1997) J Am Chem Soc 119: 1496-1497


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
A, B
6N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DM1
Query on DM1

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
DAUNOMYCIN
C27 H29 N O10
STQGQHZAVUOBTE-VGBVRHCVSA-N
BGC
Query on BGC

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 18.619α = 69.09
b = 20.096β = 90.4
c = 26.553γ = 108.03
Software Package:
Software NamePurpose
ULTIMAmodel building
X-PLORrefinement
R-AXISdata reduction
ULTIMAphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-01-21
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Structure summary
  • Version 1.5: 2024-04-03
    Changes: Refinement description