1kc8: Difference between revisions

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-{{Seed}}
-[[Image:1kc8.png|left|200px]]
-<!--
+==Co-crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit==
-The line below this paragraph, containing "STRUCTURE_1kc8", creates the "Structure Box" on the page.
+<StructureSection load='1kc8' size='340' side='right'caption='[[1kc8]], [[Resolution|resolution]] 3.01&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'>[[1kc8]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KC8 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]] 3.01&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLS:BLASTICIDIN+S'>BLS</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_1kc8|  PDB=1kc8  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kc8 OCA], [https://pdbe.org/1kc8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kc8 RCSB], [https://www.ebi.ac.uk/pdbsum/1kc8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kc8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A]
+== 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/kc/1kc8_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1kc8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Structures of anisomycin, chloramphenicol, sparsomycin, blasticidin S, and virginiamycin M bound to the large ribosomal subunit of Haloarcula marismortui have been determined at 3.0A resolution. Most of these antibiotics bind to sites that overlap those of either peptidyl-tRNA or aminoacyl-tRNA, consistent with their functioning as competitive inhibitors of peptide bond formation. Two hydrophobic crevices, one at the peptidyl transferase center and the other at the entrance to the peptide exit tunnel play roles in binding these antibiotics. Midway between these crevices, nucleotide A2103 of H.marismortui (2062 Escherichia coli) varies in its conformation and thereby contacts antibiotics bound at either crevice. The aromatic ring of anisomycin binds to the active-site hydrophobic crevice, as does the aromatic ring of puromycin, while the aromatic ring of chloramphenicol binds to the exit tunnel hydrophobic crevice. Sparsomycin contacts primarily a P-site bound substrate, but also extends into the active-site hydrophobic crevice. Virginiamycin M occupies portions of both the A and P-site, and induces a conformational change in the ribosome. Blasticidin S base-pairs with the P-loop and thereby mimics C74 and C75 of a P-site bound tRNA.
-===Co-crystal Structure of Blasticidin S Bound to the 50S Ribosomal Subunit===
+Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit.,Hansen JL, Moore PB, Steitz TA J Mol Biol. 2003 Jul 25;330(5):1061-75. PMID:12860128<ref>PMID:12860128</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1kc8" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12860128}}, adds the Publication Abstract to the page
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12860128 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12860128}}
+__TOC__
+</StructureSection>
-==About this Structure==
-KC8 is a 30 chains structure of sequences from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KC8 OCA].
-==Reference==
-<ref group="xtra">PMID:12860128</ref><references group="xtra"/>
 [[Category: Haloarcula marismortui]]
-[[Category: Ban, N.]]
+[[Category: Large Structures]]
-[[Category: Hansen, J L.]]
+[[Category: Ban N]]
-[[Category: Moore, P B.]]
+[[Category: Hansen JL]]
-[[Category: Nissen, P.]]
+[[Category: Moore PB]]
-[[Category: Steitz, T A.]]
+[[Category: Nissen P]]
-[[Category: 50s subunit]]
+[[Category: Steitz TA]]
-[[Category: Antibiotic]]
-[[Category: Blasticidin s]]
-[[Category: P-loop]]
-[[Category: P-site]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 19:41:25 2009''