2F4U | pdb_00002f4u

Asite RNA + designer antibiotic

• PDB DOI: https://doi.org/10.2210/pdb2F4U/pdb
• NAKB: 2F4U

• Classification: RNA
• Mutation(s): No 


• Deposited: 2005-11-24 Released: 2006-05-02 
• Deposition Author(s): Murray, J.B., Meroueh, S.O., Russell, R.J., Lentzen, G., Haddad, J., Mobashery, S.

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Experimental Data Snapshot

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

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

• PubMed: 16492561 
• DOI: https://doi.org/10.1016/j.chembiol.2005.11.004
• Primary Citation Related Structures: 
  2F4S, 2F4T, 2F4U, 2F4V


• 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. 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.

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Organizational Affiliation: 
• Vernalis (R&D), Ltd., Granta Park, Cambridge, UK. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.01 kDa 
• Atom Count: 960 
• Modeled Residue Count: 42 
• Deposited Residue Count: 42 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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, B	21	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AB6	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

Experimental Data & Validation

Experimental Data

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

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.1	α = 90
b = 46.46	β = 90
c = 89.5	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-02 
Deposition Author(s): Murray, J.B., Meroueh, S.O., Russell, R.J., Lentzen, G., Haddad, J., Mobashery, S.

Revision History  

• 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
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations