3S4P

Crystal structure of the bacterial ribosomal decoding site complexed with an amphiphilic paromomycin O2''-ether analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.238 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Inhibition of aminoglycoside-deactivating enzymes APH(3')-IIIa and AAC(6')-Ii by amphiphilic paromomycin O2''-ether analogues

Szychowski, J.Kondo, J.Zahr, O.Auclair, K.Westhof, E.Hanessian, S.Keillor, J.W.

(2011) ChemMedChem 6: 1961-1966


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')A, B 21N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JS6
Query on JS6

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-2-O-{2-[(2-phenylethyl)amino]ethyl}-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside
C33 H58 N6 O14
RYWOYAQAVIFICV-KWRLVFCDSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
JS6 PDBBind:  3S4P Ki: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.189α = 90
b = 44.689β = 90
c = 94.585γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction
CrystalCleardata 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: 2011-09-21
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references