3der: Difference between revisions

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-{{Seed}}
-[[Image:3der.jpg|left|200px]]
-<!--
+==Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Lys dipeptide==
-The line below this paragraph, containing "STRUCTURE_3der", creates the "Structure Box" on the page.
+<StructureSection load='3der' size='340' side='right'caption='[[3der]], [[Resolution|resolution]] 1.90&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'>[[3der]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DER 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]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_3der|  PDB=3der  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3der FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3der OCA], [https://pdbe.org/3der PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3der RCSB], [https://www.ebi.ac.uk/pdbsum/3der PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3der ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AEEP_THEMA AEEP_THEMA] Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of a broad range of other dipeptides; is most efficient with L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His.<ref>PMID:19000819</ref>
+== 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/de/3der_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=3der ConSurf].
+<div style="clear:both"></div>
-===Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Lys dipeptide===
+==See Also==
+*[[Muconate cycloisomerase|Muconate cycloisomerase]]
+== References ==
-<!--
+<references/>
-The line below this paragraph, {{ABSTRACT_PUBMED_19000819}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 19000819 is the PubMed ID number.
+</StructureSection>
--->
+[[Category: Large Structures]]
-{{ABSTRACT_PUBMED_19000819}}
+[[Category: Thermotoga maritima MSB8]]
+[[Category: Almo SC]]
-==About this Structure==
+[[Category: Fedorov AA]]
-DER is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermotoga_maritima_msb8 Thermotoga maritima msb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DER OCA].
+[[Category: Fedorov EV]]
+[[Category: Gerlt JA]]
-==Reference==
+[[Category: Imker HJ]]
-Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening., Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP, Structure. 2008 Nov;16(11):1668-77. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19000819 19000819]
-[[Category: Thermotoga maritima msb8]]
-[[Category: Almo, S C.]]
-[[Category: Fedorov, A A.]]
-[[Category: Fedorov, E V.]]
-[[Category: Gerlt, J A.]]
-[[Category: Imker, H J.]]
-[[Category: Dipeptide epimerase]]
-[[Category: Enzymatic function]]
-[[Category: Isomerase]]
-[[Category: Thermotoga maritima]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Nov 27 13:36:23 2008''