1O9M

The Complex of a novel antibiotic with the Aminoacyl Site of the Bacterial Ribosome Revealed by X-Ray Crystallography.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Complex of a Designer Antibiotic with a Model Aminoacyl Site of the 30S Ribosomal Subunit Revealed by X-Ray Crystallography

Russell, R.Murray, J.B.Lentzen, G.Haddad, J.Mobashery, S.

(2003) J.Am.Chem.Soc. 125: 3410

  • DOI: 10.1021/ja029736h

  • PubMed Abstract: 
  • The ribosome is an important target for aminoglycoside antibiotics; however, the clinical effectiveness of aminoglycosides has diminished due to bacterial resistance mechanisms. Here we report the X-ray structure of a novel synthetic aminoglycoside b ...

    The ribosome is an important target for aminoglycoside antibiotics; however, the clinical effectiveness of aminoglycosides has diminished due to bacterial resistance mechanisms. Here we report the X-ray structure of a novel synthetic aminoglycoside bound to the A site of the ribosome, its target for manifestation of activity. The structure validates the in silico design paradigms for the antibiotic and reveals the molecular interactions made by this novel antibiotic in prokaryotes.


    Organizational Affiliation

    RiboTargets, Granta Park, Cambridge CB1 6GB, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
EUBACTERIAL A-SITEA,B22Escherichia coli
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
42B
Query on 42B

Download SDF File 
Download CCD File 
B
4-AMINO-2-HYDROXYBUTANOIC ACID
C4 H9 N O3
IVUOMFWNDGNLBJ-GSVOUGTGSA-N
 Ligand Interaction
BDG
Query on BDG

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Download CCD File 
B
O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE
C6 H14 N2 O4
SQTHUUHOUPJYLK-UKFBFLRUSA-N
 Ligand Interaction
P24
Query on P24

Download SDF File 
Download CCD File 
B
1-(AMINOETHYL)AMINO-4-AMINOBUTANE
PA(24)
C6 H17 N3
VRPPEXGZBZBARW-UHFFFAOYSA-N
 Ligand Interaction
PA2
Query on PA2

Download SDF File 
Download CCD File 
B
PAROMOMYCIN (RING 2)
C6 H14 N2 O2
QOLDZWBHLDQIJR-FSIIMWSLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.800α = 90.00
b = 46.550β = 90.00
c = 88.810γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance