1J7T

Complex between Paromomycin and the 16S-rRNA A-site at 2.5 A resolution

  • Classification: RNA
  • Mutation(s): No 

  • Deposited: 2001-05-18 Released: 2002-05-18 
  • Deposition Author(s): Vicens, Q., Westhof, E.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site.

Vicens, Q.Westhof, E.

(2001) Structure 9: 647-658

  • DOI: 10.1016/s0969-2126(01)00629-3
  • Primary Citation of Related Structures:  
    1J7T

  • PubMed Abstract: 
  • Aminoglycoside antibiotics interfere with translation in both gram-positive and gram-negative bacteria by binding to the tRNA decoding A site of the 16S ribosomal RNA.


    Organizational Affiliation

    Institut de Biologie Moléculaire et Cellulaire du CNRS, Modélisation et simulations des Acides Nucléiques, UPR 9002, 15 rue René Descartes, Cedex 67084, Strasbourg, France.



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'A, B 22N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33α = 90
b = 45.9β = 90
c = 95.3γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-05-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance