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| - | [[Image:2f4u.gif|left|200px]] | |
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| - | {{Structure
| + | ==Asite RNA + designer antibiotic== |
| - | |PDB= 2f4u |SIZE=350|CAPTION= <scene name='initialview01'>2f4u</scene>, resolution 2.600Å
| + | <StructureSection load='2f4u' size='340' side='right'caption='[[2f4u]], [[Resolution|resolution]] 2.60Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=AB6:(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'>AB6</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>
| + | <table><tr><td colspan='2'>[[2f4u]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F4U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F4U FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AB6:(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'>AB6</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f4u OCA], [https://pdbe.org/2f4u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f4u RCSB], [https://www.ebi.ac.uk/pdbsum/2f4u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f4u ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[2f4s|2F4S]], [[2f4t|2F4T]], [[2f4v|2F4V]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f4u OCA], [http://www.ebi.ac.uk/pdbsum/2f4u PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2f4u RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''Asite RNA + designer antibiotic'''
| + | [[Category: Haddad J]] |
| - | | + | [[Category: Lentzen G]] |
| - | | + | [[Category: Meroueh SO]] |
| - | ==Overview==
| + | [[Category: Mobashery S]] |
| - | 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.
| + | [[Category: Murray JB]] |
| - | | + | [[Category: Russell RJ]] |
| - | ==About this Structure==
| + | |
| - | 2F4U 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=2F4U OCA].
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| - | | + | |
| - | ==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.]] | + | |
| - | [[Category: Meroueh, S O.]] | + | |
| - | [[Category: Mobashery, S.]] | + | |
| - | [[Category: Murray, J B.]] | + | |
| - | [[Category: Russell, R J.]] | + | |
| - | [[Category: asite rna]]
| + | |
| - | [[Category: designer antibiotic]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:57:54 2008''
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