2dkj: Difference between revisions

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-[[Image:2dkj.gif|left|200px]]<br /><applet load="2dkj" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2dkj, resolution 1.15&Aring;" />
-'''Crystal Structure of T.th.HB8 Serine Hydroxymethyltransferase'''<br />
-==About this Structure==
+==Crystal Structure of T.th.HB8 Serine Hydroxymethyltransferase==
-DKJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=PLP:'>PLP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.1 2.1.2.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKJ OCA].
+<StructureSection load='2dkj' size='340' side='right'caption='[[2dkj]], [[Resolution|resolution]] 1.15&Aring;' scene=''>
-[[Category: Glycine hydroxymethyltransferase]]
+== Structural highlights ==
-[[Category: Single protein]]
+<table><tr><td colspan='2'>[[2dkj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKJ FirstGlance]. <br>
-[[Category: Thermus thermophilus]]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.15&#8491;</td></tr>
-[[Category: Goto, M.]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-[[Category: Hirotsu, K.]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkj OCA], [https://pdbe.org/2dkj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkj RCSB], [https://www.ebi.ac.uk/pdbsum/2dkj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkj ProSAT], [https://www.topsan.org/Proteins/RSGI/2dkj TOPSAN]</span></td></tr>
-[[Category: Kai, K.]]
+</table>
-[[Category: Miyahara, I.]]
+== Function ==
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[https://www.uniprot.org/uniprot/GLYA_THET8 GLYA_THET8] Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.[HAMAP-Rule:MF_00051]
-[[Category: PLP]]
+== Evolutionary Conservation ==
-[[Category: SO4]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: national project on protein structural and functional analyses]]
+Check<jmol>
-[[Category: nppsfa]]
+  <jmolCheckbox>
-[[Category: plp dependent enzyme]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/2dkj_consurf.spt"</scriptWhenChecked>
-[[Category: riken structural genomics/proteomics initiative]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: rsgi]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: structural genomics]]
+  </jmolCheckbox>
-[[Category: transferase]]
+</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=2dkj ConSurf].
+<div style="clear:both"></div>
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:59:41 2008''
+==See Also==
+*[[Serine hydroxymethyltransferase 3D structures|Serine hydroxymethyltransferase 3D structures]]
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Thermus thermophilus HB8]]
+[[Category: Goto M]]
+[[Category: Hirotsu K]]
+[[Category: Kai K]]
+[[Category: Miyahara I]]