1kd1
From Proteopedia
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==Co-crystal Structure of Spiramycin bound to the 50S Ribosomal Subunit of Haloarcula marismortui== | ==Co-crystal Structure of Spiramycin bound to the 50S Ribosomal Subunit of Haloarcula marismortui== | ||
| - | <StructureSection load='1kd1' size='340' side='right' caption='[[1kd1]], [[Resolution|resolution]] 3.00Å' scene=''> | + | <StructureSection load='1kd1' size='340' side='right'caption='[[1kd1]], [[Resolution|resolution]] 3.00Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1kd1]] is a | + | <table><tr><td colspan='2'>[[1kd1]] 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=1KD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KD1 FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>, <scene name='pdbligand=SPR:SPIRAMYCIN+I'>SPR</scene | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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>, <scene name='pdbligand=SPR:SPIRAMYCIN+I'>SPR</scene></td></tr> | |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kd1 OCA], [https://pdbe.org/1kd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kd1 RCSB], [https://www.ebi.ac.uk/pdbsum/1kd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kd1 ProSAT]</span></td></tr> |
| - | <table> | + | </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 == | == 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/kd/1kd1_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kd/1kd1_consurf.spt"</scriptWhenChecked> |
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1kd1 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 1kd1" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Ribosome 3D structures|Ribosome 3D structures]] | *[[Ribosome 3D structures|Ribosome 3D structures]] | ||
| - | *[[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin|User:Wayne Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Haloarcula marismortui]] | [[Category: Haloarcula marismortui]] | ||
| - | [[Category: Ban | + | [[Category: Large Structures]] |
| - | [[Category: Hansen | + | [[Category: Ban N]] |
| - | [[Category: Ippolito | + | [[Category: Hansen JL]] |
| - | [[Category: Moore | + | [[Category: Ippolito JA]] |
| - | [[Category: Nissen | + | [[Category: Moore PB]] |
| - | [[Category: Steitz | + | [[Category: Nissen P]] |
| - | + | [[Category: Steitz TA]] | |
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Current revision
Co-crystal Structure of Spiramycin bound to the 50S Ribosomal Subunit of Haloarcula marismortui
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