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3dll
From Proteopedia
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==The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning== | ==The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning== | ||
| - | <StructureSection load='3dll' size='340' side='right' caption='[[3dll]], [[Resolution|resolution]] 3.50Å' scene=''> | + | <StructureSection load='3dll' size='340' side='right'caption='[[3dll]], [[Resolution|resolution]] 3.50Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[3dll]] is a | + | <table><tr><td colspan='2'>[[3dll]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DLL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DLL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZLD:N-{[(5S)-3-(3-FLUORO-4-MORPHOLIN-4-YLPHENYL)-2-OXO-1,3-OXAZOLIDIN-5-YL]METHYL}ACETAMIDE'>ZLD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.5Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZLD:N-{[(5S)-3-(3-FLUORO-4-MORPHOLIN-4-YLPHENYL)-2-OXO-1,3-OXAZOLIDIN-5-YL]METHYL}ACETAMIDE'>ZLD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dll OCA], [https://pdbe.org/3dll PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dll RCSB], [https://www.ebi.ac.uk/pdbsum/3dll PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dll ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/RL2_DEIRA RL2_DEIRA] 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_B] | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/3dll_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/3dll_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/ | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | + | </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=3dll ConSurf]. |
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
| + | <div class="pdbe-citations 3dll" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Deinococcus radiodurans]] | [[Category: Deinococcus radiodurans]] | ||
| - | [[Category: Connell | + | [[Category: Large Structures]] |
| - | [[Category: Fucini | + | [[Category: Connell SR]] |
| - | [[Category: Harms | + | [[Category: Fucini P]] |
| - | [[Category: Schluenzen | + | [[Category: Harms JM]] |
| - | [[Category: Starosta | + | [[Category: Schluenzen F]] |
| - | [[Category: Wilson | + | [[Category: Starosta AL]] |
| - | + | [[Category: Wilson DN]] | |
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Current revision
The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning
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