2f4v: Difference between revisions

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-[[Image:2f4v.png|left|200px]]
-<!--
+==30S ribosome + designer antibiotic==
-The line below this paragraph, containing "STRUCTURE_2f4v", creates the "Structure Box" on the page.
+<StructureSection load='2f4v' size='340' side='right'caption='[[2f4v]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2f4v]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F4V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F4V FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=D2C:(2S,4S,4AR,5AS,6S,11R,11AS,12R,12AR)-7-CHLORO-4-(DIMETHYLAMINO)-6,10,11,12-TETRAHYDROXY-1,3-DIOXO-1,2,3,4,4A,5,5A,6,11,11A,12,12A-DODECAHYDROTETRACENE-2-CARBOXAMIDE'>D2C</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2f4v|  PDB=2f4v  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f4v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f4v OCA], [https://pdbe.org/2f4v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f4v RCSB], [https://www.ebi.ac.uk/pdbsum/2f4v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f4v ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f4/2f4v_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2f4v ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-===30S ribosome + designer antibiotic===
+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<ref>PMID:16492561</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16492561}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2f4v" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16492561 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_16492561}}
-==About this Structure==
-[[2f4v]] is a 21 chain structure of [[Ribosomal protein S10]], [[Ribosomal protein S11]], [[Ribosomal protein S12]], [[Ribosomal protein S13]], [[Ribosomal protein S15]], [[Ribosomal protein S17]], [[Ribosomal protein S2]], [[Ribosomal protein S20]], [[Ribosomal protein S3]] and [[Ribosomal protein S4]] with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F4V OCA].
 ==See Also==
-*[[Ribosomal protein S10]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-*[[Ribosomal protein S11]]
+== References ==
-*[[Ribosomal protein S12]]
+<references/>
-*[[Ribosomal protein S13]]
+__TOC__
-*[[Ribosomal protein S15]]
+</StructureSection>
-*[[Ribosomal protein S17]]
+[[Category: Large Structures]]
-*[[Ribosomal protein S2]]
-*[[Ribosomal protein S20]]
-*[[Ribosomal protein S3]]
-*[[Ribosomal protein S4]]
-==Reference==
-<ref group="xtra">PMID:16492561</ref><references group="xtra"/>
 [[Category: Thermus thermophilus]]
-[[Category: Haddad, J.]]
+[[Category: Haddad J]]
-[[Category: Lentzen, G.]]
+[[Category: Lentzen G]]
-[[Category: Meroueh, S O.]]
+[[Category: Meroueh SO]]
-[[Category: Mobashery, S.]]
+[[Category: Mobashery S]]
-[[Category: Murray, J B.]]
+[[Category: Murray JB]]
-[[Category: Russell, R J.]]
+[[Category: Russell RJ]]
-[[Category: 30s ribosome subunit]]
-[[Category: Designer antibiotic]]