4P20

Crystal structures of the bacterial ribosomal decoding site complexed with amikacin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.213 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the gamma-amino-alpha-hydroxybutyryl (haba) group.

Kondo, J.Francois, B.Russell, R.J.Murray, J.B.Westhof, E.

(2006) Biochimie 88: 1027-1031

  • DOI: https://doi.org/10.1016/j.biochi.2006.05.017
  • Primary Citation of Related Structures:  
    4P20

  • PubMed Abstract: 

    Amikacin is the 4,6-linked aminoglycoside modified at position N1 of the 2-deoxystreptamine ring (ring II) by the L-haba group. In the present study, the crystal structure of a complex between oligonucleotide containing the bacterial ribosomal A site and amikacin has been solved at 2.7 A resolution. Amikacin specifically binds to the A site in practically the same way as its parent compound kanamycin. In addition, the L-haba group interacts with the upper side of the A site through two direct contacts, O2*...H-N4(C1496) and N4*-H...O6(G1497). The present crystal structure shows how the introduction of the L-haba group on ring II of aminoglycoside is an effective mutation for obtaining a higher affinity to the bacterial A site.


  • Organizational Affiliation

    Institut de Biologie Moléculaire et Cellulaire, UPR9002 CNRS, Université Louis-Pasteur, 15, rue René-Descartes, 67084 Strasbourg, France.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
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
23synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AKN
Query on AKN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide
C22 H43 N5 O13
LKCWBDHBTVXHDL-RMDFUYIESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.55α = 90
b = 32.82β = 108.71
c = 52.66γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2015-01-07
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary