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3ekm
From Proteopedia
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==Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP== | ==Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP== | ||
| - | <StructureSection load='3ekm' size='340' side='right' caption='[[3ekm]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='3ekm' size='340' side='right'caption='[[3ekm]], [[Resolution|resolution]] 2.30Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[3ekm]] is a 6 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[3ekm]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EKM FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZDR:(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC+ACID'>ZDR</scene></td></tr> | |
| - | <tr id=' | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ekm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ekm OCA], [https://pdbe.org/3ekm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ekm RCSB], [https://www.ebi.ac.uk/pdbsum/3ekm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ekm ProSAT]</span></td></tr> |
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | |
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/DAPF_ARATH DAPF_ARATH] Racemase that operates by a 'two-base' mechanism, which involves one active-site cysteine acting as a base to abstract the alpha-proton of an amino acid, while a second cysteine thiol functions as an acid to reprotonate the resulting planar carbanionic intermediate from the opposite face.<ref>PMID:15652176</ref> | ||
== 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/ek/3ekm_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ek/3ekm_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=3ekm 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 3ekm" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Arabidopsis thaliana]] | [[Category: Arabidopsis thaliana]] | ||
| - | [[Category: | + | [[Category: Large Structures]] |
| - | + | [[Category: Cherney MM]] | |
| - | [[Category: Cherney | + | [[Category: James MNG]] |
| - | [[Category: James | + | [[Category: Moorthie VA]] |
| - | [[Category: Moorthie | + | [[Category: Pillai B]] |
| - | [[Category: Pillai | + | [[Category: Vederas JC]] |
| - | [[Category: Vederas | + | [[Category: Van Belkum MJ]] |
| - | [[Category: | + | |
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Current revision
Crystal structure of diaminopimelate epimerase form arabidopsis thaliana in complex with irreversible inhibitor DL-AziDAP
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