2f4t: Difference between revisions

Revision as of 03:27, 4 May 2008

Asite RNA + designer antibiotic

OverviewOverview

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.

About this StructureAbout this Structure

Full crystallographic information is available from OCA.

ReferenceReference

Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site., Murray JB, Meroueh SO, Russell RJ, Lentzen G, Haddad J, Mobashery S, Chem Biol. 2006 Feb;13(2):129-38. PMID:16492561 Page seeded by OCA on Sun May 4 03:27:38 2008

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OCA

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 [[Image:2f4t.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 2f4t |SIZE=350|CAPTION= <scene name='initialview01'>2f4t</scene>, resolution 3.000&Aring;
+The line below this paragraph, containing "STRUCTURE_2f4t", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=AB9:(2R)-4-AMINO-N-{(1R,2S,3R,4R,5S)-5-AMINO-2-{2-[(2-AMINOETHYL)AMINO]ETHOXY}-4-[(2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-3-HYDROXYCYCLOHEXYL}-2-HYDROXYBUTANAMIDE'>AB9</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY=
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_2f4t|  PDB=2f4t  |  SCENE=  }}
-|RELATEDENTRY=[[2f4s|2F4S]], [[2f4u|2F4U]], [[2f4v|2F4V]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f4t OCA], [http://www.ebi.ac.uk/pdbsum/2f4t PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2f4t RCSB]</span>
-}}
 '''Asite RNA + designer antibiotic'''
@@ Line 19: / Line 16: @@
 ==About this Structure==
-F4T is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F4T OCA].
+Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F4T OCA].
 ==Reference==
 Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site., Murray JB, Meroueh SO, Russell RJ, Lentzen G, Haddad J, Mobashery S, Chem Biol. 2006 Feb;13(2):129-38. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16492561 16492561]
-[[Category: Protein complex]]
 [[Category: Haddad, J.]]
 [[Category: Lentzen, G.]]
@@ Line 30: / Line 26: @@
 [[Category: Murray, J B.]]
 [[Category: Russell, R J.]]
-[[Category: asite rna]]
+[[Category: Asite rna]]
-[[Category: designer antibiotic]]
+[[Category: Designer antibiotic]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 03:27:38 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:57:54 2008''