2F4U

Asite RNA + designer antibiotic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.299 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site

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

(2006) Chem Biol 13: 129-138

  • DOI: 10.1016/j.chembiol.2005.11.004
  • Primary Citation of Related Structures:  
    2F4V, 2F4U, 2F4T, 2F4S

  • PubMed Abstract: 
  • The X-ray crystal structures for the complexes of three designer antibiotics, compounds 1, 2, and 3, bound to two models for the ribosomal aminoacyl-tRNA site (A site) at 2.5-3.0 Angstroms resolution and that of neamine at 2.8 Angstroms resolution are described ...

    The X-ray crystal structures for the complexes of three designer antibiotics, compounds 1, 2, and 3, bound to two models for the ribosomal aminoacyl-tRNA site (A site) at 2.5-3.0 Angstroms resolution and that of neamine at 2.8 Angstroms resolution are described. Furthermore, the complex of antibiotic 1 bound to the A site in the entire 30S ribosomal subunit of Thermus thermophilus is reported at 3.8 Angstroms resolution. Molecular dynamics simulations revealed that the designer compounds provide additional stability to bases A1492 and A1493 in their extrahelical forms. Snapshots from the simulations were used for free energy calculations, which revealed that van der Waals and hydrophobic effects were the driving forces behind the binding of designer antibiotic 3 when compared to the parental neamine.


    Organizational Affiliation

    Vernalis (R&D), Ltd., Granta Park, Cambridge, UK. j.murray@vernalis.com



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'A, B21N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AB6 (Subject of Investigation/LOI)
Query on AB6

Download Ideal Coordinates CCD File 
C [auth B](2R)-4-AMINO-N-((1R,2S,3R,4R,5S)-5-AMINO-4-[(2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-{2-[(3-AMINOPROPYL)AMINO]ETHOXY}-3-HYDROXYCYCLOHEXYL)-2-HYDROXYBUTANAMIDE
C21 H44 N6 O9
MJKNCJCIMZKDAF-BORACOTDSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
AB6 PDBBind:  2F4U Kd: 5900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.299 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.1α = 90
b = 46.46β = 90
c = 89.5γ = 90
Software Package:
Software NamePurpose
d*TREKdata processing
CNSrefinement
PDB_EXTRACTdata extraction
d*TREKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-02
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance