2O3X

Crystal Structure of the Prokaryotic Ribosomal Decoding Site Complexed with Paromamine Derivative NB30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.246 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Differential Selectivity of Natural and Synthetic Aminoglycosides towards the Eukaryotic and Prokaryotic Decoding A Sites.

Kondo, J.Hainrichson, M.Nudelman, I.Shallom-Shezifi, D.Barbieri, C.M.Pilch, D.S.Westhof, E.Baasov, T.

(2007) Chembiochem 8: 1700-1709

  • DOI: https://doi.org/10.1002/cbic.200700271
  • Primary Citation of Related Structures:  
    2O3V, 2O3W, 2O3X, 2O3Y

  • PubMed Abstract: 

    The lack of absolute prokaryotic selectivity of natural antibiotics is widespread and is a significant clinical problem. The use of this disadvantage of aminoglycoside antibiotics for the possible treatment of human genetic diseases is extremely challenging. Here, we have used a combination of biochemical and structural analysis to compare and contrast the molecular mechanisms of action and the structure-activity relationships of a new synthetic aminoglycoside, NB33, and a structurally similar natural aminoglycoside apramycin. The data presented herein demonstrate the general molecular principles that determine the decreased selectivity of apramycin for the prokaryotic decoding site, and the increased selectivity of NB33 for the eukaryotic decoding site. These results are therefore extremely beneficial for further research on both the design of new aminoglycoside-based antibiotics with diminished deleterious effects on humans, as well as the design of new aminoglycoside-based structures that selectively target the eukaryotic ribosome.


  • Organizational Affiliation

    Architecture et Réactivité de l'ARN, Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, CNRS, 15 rue René Descartes, 67084 Strasbourg, France.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')
A, B
23N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N30
Query on N30

Download Ideal Coordinates CCD File 
C [auth B](1R,2R,3S,4R,6S)-4,6-DIAMINO-2-[(5-AMINO-5-DEOXY-BETA-D-RIBOFURANOSYL)OXY]-3-HYDROXYCYCLOHEXYL 2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSIDE
C17 H34 N4 O10
FNBQIDOUCINBIA-VVPCINPTSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
N30 PDBBind:  2O3X Kd: 5.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.14α = 90
b = 46.83β = 90
c = 85.72γ = 90
Software Package:
Software NamePurpose
d*TREKdata processing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description