2zdx - Revision history

OCA at 13:33, 1 November 2023

2023-11-01T13:33:00Z

←Older revision		Revision as of 13:33, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='2zdx' size='340' side='right'caption='[[2zdx]], [[Resolution\|resolution]] 2.54Å' scene=''>		<StructureSection load='2zdx' size='340' side='right'caption='[[2zdx]], [[Resolution\|resolution]] 2.54Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zdx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZDX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zdx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZDX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=P4A:4~~-~~[4-(4-METHOXYPHENYL)-5-METHYL-1H-PYRAZOL-3-YL]BENZENE-1~~,~~3-DIOL'>P4A</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]] 2.54Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[2zdy\|2zdy]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=P4A:4-[4-(4-METHOXYPHENYL)-5-METHYL-1H-PYRAZOL-3-YL]BENZENE-1,3-DIOL'>P4A</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PDK4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=9606 HUMAN])</td></tr>~~	+
-	~~<tr id='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/~~[~~Pyruvate_dehydrogenase_~~(~~acetyl~~-~~transferring~~)]~~_kinase [Pyruvate dehydrogenase (acetyl~~-~~transferring)] kinase]~~, ~~with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=2.7.11.2 2.7.11.2]~~ </~~span~~></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=2zdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdx OCA], [https://pdbe.org/2zdx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zdx RCSB], [https://www.ebi.ac.uk/pdbsum/2zdx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zdx ProSAT]</span></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=2zdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdx OCA], [https://pdbe.org/2zdx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zdx RCSB], [https://www.ebi.ac.uk/pdbsum/2zdx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zdx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PDK4_HUMAN PDK4_HUMAN]] Serine/threonine kinase that plays a key role in regulation of glucose and fatty acid metabolism and homeostasis via phosphorylation of the pyruvate dehydrogenase subunits PDHA1 and PDHA2. This inhibits pyruvate dehydrogenase activity, and thereby regulates metabolite flux through the tricarboxylic acid cycle, down-regulates aerobic respiration and inhibits the formation of acetyl-coenzyme A from pyruvate. Inhibition of pyruvate dehydrogenase decreases glucose utilization and increases fat metabolism in response to prolonged fasting and starvation. Plays an important role in maintaining normal blood glucose levels under starvation, and is involved in the insulin signaling cascade. Via its regulation of pyruvate dehydrogenase activity, plays an important role in maintaining normal blood pH and in preventing the accumulation of ketone bodies under starvation. In the fed state, mediates cellular responses to glucose levels and to a high-fat diet. Regulates both fatty acid oxidation and de novo fatty acid biosynthesis. Plays a role in the generation of reactive oxygen species. Protects detached epithelial cells against anoikis. Plays a role in cell proliferation via its role in regulating carbohydrate and fatty acid metabolism.<ref>PMID:15955060</ref> <ref>PMID:21852536</ref> <ref>PMID:21816445</ref> <ref>PMID:18658136</ref>	+	[https://www.uniprot.org/uniprot/PDK4_HUMAN PDK4_HUMAN] Serine/threonine kinase that plays a key role in regulation of glucose and fatty acid metabolism and homeostasis via phosphorylation of the pyruvate dehydrogenase subunits PDHA1 and PDHA2. This inhibits pyruvate dehydrogenase activity, and thereby regulates metabolite flux through the tricarboxylic acid cycle, down-regulates aerobic respiration and inhibits the formation of acetyl-coenzyme A from pyruvate. Inhibition of pyruvate dehydrogenase decreases glucose utilization and increases fat metabolism in response to prolonged fasting and starvation. Plays an important role in maintaining normal blood glucose levels under starvation, and is involved in the insulin signaling cascade. Via its regulation of pyruvate dehydrogenase activity, plays an important role in maintaining normal blood pH and in preventing the accumulation of ketone bodies under starvation. In the fed state, mediates cellular responses to glucose levels and to a high-fat diet. Regulates both fatty acid oxidation and de novo fatty acid biosynthesis. Plays a role in the generation of reactive oxygen species. Protects detached epithelial cells against anoikis. Plays a role in cell proliferation via its role in regulating carbohydrate and fatty acid metabolism.<ref>PMID:15955060</ref> <ref>PMID:21852536</ref> <ref>PMID:21816445</ref> <ref>PMID:18658136</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kawamoto, M]]	+	[[Category: Kawamoto M]]
-	[[Category: Kukimoto-niino, M]]	+	[[Category: Kukimoto-niino M]]
-	[[Category: Matsusue, T]]	+	[[Category: Matsusue T]]
-	[[Category: Shiromizu, I]]	+	[[Category: Shiromizu I]]
-	[[Category: Shirouzu, M]]	+	[[Category: Shirouzu M]]
-	[[Category: Terada, T]]	+	[[Category: Terada T]]
-	[[Category: Tokmakov, A]]	+	[[Category: Tokmakov A]]
-	[[Category: Yokoyama, S]]	+	[[Category: Yokoyama S]]
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Carbohydrate metabolism]]~~	+
-	~~[[Category: Glucose metabolism]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Mitochondrion]]~~	+
-	~~[[Category: Pdk4]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transit peptide~~]]	+

OCA at 10:51, 8 December 2021

2021-12-08T10:51:06Z

←Older revision		Revision as of 10:51, 8 December 2021
Line 1:		Line 1:

	==Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4==		==Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4==
-	<StructureSection load='2zdx' size='340' side='right' caption='[[2zdx]], [[Resolution\|resolution]] 2.54Å' scene=''>	+	<StructureSection load='2zdx' size='340' side='right'caption='[[2zdx]], [[Resolution\|resolution]] 2.54Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zdx]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ZDX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zdx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZDX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=P4A:4-[4-(4-METHOXYPHENYL)-5-METHYL-1H-PYRAZOL-3-YL]BENZENE-1,3-DIOL'>P4A</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=P4A:4-[4-(4-METHOXYPHENYL)-5-METHYL-1H-PYRAZOL-3-YL]BENZENE-1,3-DIOL'>P4A</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zdy\|2zdy]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2zdy\|2zdy]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDK4 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDK4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]_kinase [Pyruvate dehydrogenase (acetyl-transferring)] kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.2 2.7.11.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]_kinase [Pyruvate dehydrogenase (acetyl-transferring)] kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.2 2.7.11.2] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2zdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdx OCA], [~~http~~://pdbe.org/2zdx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2zdx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2zdx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2zdx ProSAT]</span></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=2zdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdx OCA], [https://pdbe.org/2zdx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zdx RCSB], [https://www.ebi.ac.uk/pdbsum/2zdx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zdx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PDK4_HUMAN PDK4_HUMAN]] Serine/threonine kinase that plays a key role in regulation of glucose and fatty acid metabolism and homeostasis via phosphorylation of the pyruvate dehydrogenase subunits PDHA1 and PDHA2. This inhibits pyruvate dehydrogenase activity, and thereby regulates metabolite flux through the tricarboxylic acid cycle, down-regulates aerobic respiration and inhibits the formation of acetyl-coenzyme A from pyruvate. Inhibition of pyruvate dehydrogenase decreases glucose utilization and increases fat metabolism in response to prolonged fasting and starvation. Plays an important role in maintaining normal blood glucose levels under starvation, and is involved in the insulin signaling cascade. Via its regulation of pyruvate dehydrogenase activity, plays an important role in maintaining normal blood pH and in preventing the accumulation of ketone bodies under starvation. In the fed state, mediates cellular responses to glucose levels and to a high-fat diet. Regulates both fatty acid oxidation and de novo fatty acid biosynthesis. Plays a role in the generation of reactive oxygen species. Protects detached epithelial cells against anoikis. Plays a role in cell proliferation via its role in regulating carbohydrate and fatty acid metabolism.<ref>PMID:15955060</ref> <ref>PMID:21852536</ref> <ref>PMID:21816445</ref> <ref>PMID:18658136</ref>	+	[[https://www.uniprot.org/uniprot/PDK4_HUMAN PDK4_HUMAN]] Serine/threonine kinase that plays a key role in regulation of glucose and fatty acid metabolism and homeostasis via phosphorylation of the pyruvate dehydrogenase subunits PDHA1 and PDHA2. This inhibits pyruvate dehydrogenase activity, and thereby regulates metabolite flux through the tricarboxylic acid cycle, down-regulates aerobic respiration and inhibits the formation of acetyl-coenzyme A from pyruvate. Inhibition of pyruvate dehydrogenase decreases glucose utilization and increases fat metabolism in response to prolonged fasting and starvation. Plays an important role in maintaining normal blood glucose levels under starvation, and is involved in the insulin signaling cascade. Via its regulation of pyruvate dehydrogenase activity, plays an important role in maintaining normal blood pH and in preventing the accumulation of ketone bodies under starvation. In the fed state, mediates cellular responses to glucose levels and to a high-fat diet. Regulates both fatty acid oxidation and de novo fatty acid biosynthesis. Plays a role in the generation of reactive oxygen species. Protects detached epithelial cells against anoikis. Plays a role in cell proliferation via its role in regulating carbohydrate and fatty acid metabolism.<ref>PMID:15955060</ref> <ref>PMID:21852536</ref> <ref>PMID:21816445</ref> <ref>PMID:18658136</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Kawamoto, M]]		[[Category: Kawamoto, M]]
	[[Category: Kukimoto-niino, M]]		[[Category: Kukimoto-niino, M]]

OCA at 07:06, 18 October 2018

2018-10-18T07:06:04Z

←Older revision		Revision as of 07:06, 18 October 2018
Line 1:		Line 1:
		+
	==Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4==		==Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4==
	<StructureSection load='2zdx' size='340' side='right' caption='[[2zdx]], [[Resolution\|resolution]] 2.54Å' scene=''>		<StructureSection load='2zdx' size='340' side='right' caption='[[2zdx]], [[Resolution\|resolution]] 2.54Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDK4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDK4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]_kinase [Pyruvate dehydrogenase (acetyl-transferring)] kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.2 2.7.11.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]_kinase [Pyruvate dehydrogenase (acetyl-transferring)] kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.2 2.7.11.2] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdx OCA], [http://pdbe.org/2zdx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zdx RCSB], [http://www.ebi.ac.uk/pdbsum/2zdx PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdx OCA], [http://pdbe.org/2zdx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zdx RCSB], [http://www.ebi.ac.uk/pdbsum/2zdx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zdx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zd/2zdx_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zd/2zdx_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>

OCA at 00:56, 9 February 2016

2016-02-09T00:56:43Z

←Older revision		Revision as of 00:56, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='2zdx' size='340' side='right' caption='[[2zdx]], [[Resolution\|resolution]] 2.54Å' scene=''>		<StructureSection load='2zdx' size='340' side='right' caption='[[2zdx]], [[Resolution\|resolution]] 2.54Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zdx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZDX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zdx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZDX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=P4A:4-[4-(4-METHOXYPHENYL)-5-METHYL-1H-PYRAZOL-3-YL]BENZENE-1,3-DIOL'>P4A</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=P4A:4-[4-(4-METHOXYPHENYL)-5-METHYL-1H-PYRAZOL-3-YL]BENZENE-1,3-DIOL'>P4A</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zdy\|2zdy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zdy\|2zdy]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDK4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDK4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]_kinase [Pyruvate dehydrogenase (acetyl-transferring)] kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.2 2.7.11.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]_kinase [Pyruvate dehydrogenase (acetyl-transferring)] kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.2 2.7.11.2] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zdx RCSB], [http://www.ebi.ac.uk/pdbsum/2zdx PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdx OCA], [http://pdbe.org/2zdx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zdx RCSB], [http://www.ebi.ac.uk/pdbsum/2zdx PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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=2zdx ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 2zdx" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Kawamoto, M]]		[[Category: Kawamoto, M]]
	[[Category: Kukimoto-niino, M]]		[[Category: Kukimoto-niino, M]]

OCA at 03:20, 25 December 2014

2014-12-25T03:20:10Z

←Older revision		Revision as of 03:20, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2zdx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZDX FirstGlance]. <br>		<table><tr><td colspan='2'>[[2zdx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZDX FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=P4A:4-[4-(4-METHOXYPHENYL)-5-METHYL-1H-PYRAZOL-3-YL]BENZENE-1,3-DIOL'>P4A</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=P4A:4-[4-(4-METHOXYPHENYL)-5-METHYL-1H-PYRAZOL-3-YL]BENZENE-1,3-DIOL'>P4A</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zdy\|2zdy]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zdy\|2zdy]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDK4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDK4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]_kinase [Pyruvate dehydrogenase (acetyl-transferring)] kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.2 2.7.11.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]_kinase [Pyruvate dehydrogenase (acetyl-transferring)] kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.2 2.7.11.2] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zdx RCSB], [http://www.ebi.ac.uk/pdbsum/2zdx PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zdx RCSB], [http://www.ebi.ac.uk/pdbsum/2zdx PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PDK4_HUMAN PDK4_HUMAN]] Serine/threonine kinase that plays a key role in regulation of glucose and fatty acid metabolism and homeostasis via phosphorylation of the pyruvate dehydrogenase subunits PDHA1 and PDHA2. This inhibits pyruvate dehydrogenase activity, and thereby regulates metabolite flux through the tricarboxylic acid cycle, down-regulates aerobic respiration and inhibits the formation of acetyl-coenzyme A from pyruvate. Inhibition of pyruvate dehydrogenase decreases glucose utilization and increases fat metabolism in response to prolonged fasting and starvation. Plays an important role in maintaining normal blood glucose levels under starvation, and is involved in the insulin signaling cascade. Via its regulation of pyruvate dehydrogenase activity, plays an important role in maintaining normal blood pH and in preventing the accumulation of ketone bodies under starvation. In the fed state, mediates cellular responses to glucose levels and to a high-fat diet. Regulates both fatty acid oxidation and de novo fatty acid biosynthesis. Plays a role in the generation of reactive oxygen species. Protects detached epithelial cells against anoikis. Plays a role in cell proliferation via its role in regulating carbohydrate and fatty acid metabolism.<ref>PMID:15955060</ref> <ref>PMID:21852536</ref> <ref>PMID:21816445</ref> <ref>PMID:18658136</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Kawamoto, M.]]	+	[[Category: Kawamoto, M]]
-	[[Category: Kukimoto-niino, M.]]	+	[[Category: Kukimoto-niino, M]]
-	[[Category: Matsusue, T.]]	+	[[Category: Matsusue, T]]
-	[[Category: Shiromizu, I.]]	+	[[Category: Shiromizu, I]]
-	[[Category: Shirouzu, M.]]	+	[[Category: Shirouzu, M]]
-	[[Category: Terada, T.]]	+	[[Category: Terada, T]]
-	[[Category: Tokmakov, A.]]	+	[[Category: Tokmakov, A]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Carbohydrate metabolism]]		[[Category: Carbohydrate metabolism]]

OCA at 05:24, 2 October 2014

2014-10-02T05:24:28Z

←Older revision		Revision as of 05:24, 2 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2zdx\| PDB=2zdx \| SCENE= }}~~	+	==Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4==
-	===Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4===	+	<StructureSection load='2zdx' size='340' side='right' caption='[[2zdx]], [[Resolution\|resolution]] 2.54Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21904029}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2zdx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZDX FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=P4A:4-[4-(4-METHOXYPHENYL)-5-METHYL-1H-PYRAZOL-3-YL]BENZENE-1,3-DIOL'>P4A</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2zdy\|2zdy]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDK4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/[Pyruvate_dehydrogenase_(acetyl-transferring)]_kinase [Pyruvate dehydrogenase (acetyl-transferring)] kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.2 2.7.11.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zdx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zdx RCSB], [http://www.ebi.ac.uk/pdbsum/2zdx PDBsum]</span></td></tr>
		+	<table>
		+	== 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/zd/2zdx_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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The mitochondrial pyruvate dehydrogenase complex (PDC) catalyzes the oxidative decarboxylation of pyruvate to acetyl-CoA. PDC activity is tightly regulated by four members of a family of pyruvate dehydrogenase kinase isoforms (PDK1-4), which phosphorylate and inactivate PDC. Recently, the development of specific inhibitors of PDK4 has become an especially important focus for the pharmaceutical management of diabetes and obesity. In this study, crystal structures of human PDK4 complexed with either AMPPNP, ADP or the inhibitor M77976 were determined. ADP-bound PDK4 has a slightly wider active-site cleft and a more disordered ATP lid compared with AMPPNP-bound PDK4, although both forms of PDK4 assume open conformations with a wider active-site cleft than that in the closed conformation of the previously reported ADP-bound PDK2 structure. M77976 binds to the ATP-binding pocket of PDK4 and causes local conformational changes with complete disordering of the ATP lid. M77976 binding also leads to a large domain rearrangement that further expands the active-site cleft of PDK4 compared with the ADP- and AMPPNP-bound forms. Biochemical analyses revealed that M77976 inhibits PDK4 with increased potency compared with the previously characterized PDK inhibitor radicicol. Thus, the present structures demonstrate for the first time the flexible and dynamic aspects of PDK4 in the open conformation and provide a basis for the development of novel inhibitors targeting the nucleotide-binding pocket of PDK4.

-	~~==About this Structure==~~	+	Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4.,Kukimoto-Niino M, Tokmakov A, Terada T, Ohbayashi N, Fujimoto T, Gomi S, Shiromizu I, Kawamoto M, Matsusue T, Shirouzu M, Yokoyama S Acta Crystallogr D Biol Crystallogr. 2011 Sep;67(Pt 9):763-73. doi:, 10.1107/S090744491102405X. Epub 2011 Aug 9. PMID:21904029<ref>PMID:21904029</ref>
-	~~[[2zdx]] is a 2 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org~~/~~wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=2ZDX OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Pyruvate dehydrogenase kinase\|Pyruvate dehydrogenase kinase]]		*[[Pyruvate dehydrogenase kinase\|Pyruvate dehydrogenase kinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:021904029<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Kawamoto, M.]]		[[Category: Kawamoto, M.]]

OCA at 09:50, 11 March 2013

2013-03-11T09:50:00Z

←Older revision		Revision as of 09:50, 11 March 2013
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-	[[Image:2zdx.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_2zdx", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2zdx\| PDB=2zdx \| SCENE= }}		{{STRUCTURE_2zdx\| PDB=2zdx \| SCENE= }}
-
	===Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4===		===Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21904029}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21904029 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21904029}}		{{ABSTRACT_PUBMED_21904029}}

	==About this Structure==		==About this Structure==
	[[2zdx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDX OCA].		[[2zdx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDX OCA].
		+
		+	==See Also==
		+	*[[Pyruvate dehydrogenase kinase\|Pyruvate dehydrogenase kinase]]

	==Reference==		==Reference==

OCA: Protected "2zdx" [edit=sysop:move=sysop]

2011-11-23T18:18:03Z

Protected "2zdx" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:18, 23 November 2011

OCA at 18:18, 23 November 2011

2011-11-23T18:18:02Z

←Older revision		Revision as of 18:18, 23 November 2011
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-	{{Seed}}
	[[Image:2zdx.png\|left\|200px]]		[[Image:2zdx.png\|left\|200px]]

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	===Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4===		===Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21904029}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21904029 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21904029}}

	==About this Structure==		==About this Structure==
-	~~2ZDX~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDX OCA].	+	[[2zdx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZDX OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021904029</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Kawamoto, M.]]		[[Category: Kawamoto, M.]]
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	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Transit peptide]]		[[Category: Transit peptide]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 23 08:19:33 2009''

OCA at 05:19, 23 September 2009

2009-09-23T05:19:34Z

←Older revision		Revision as of 05:19, 23 September 2009
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	{{Seed}}		{{Seed}}
-	[[Image:2zdx.~~jpg~~\|left\|200px]]	+	[[Image:2zdx.png\|left\|200px]]

	<!--		<!--
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	[[Category: Transit peptide]]		[[Category: Transit peptide]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Dec 10 14~~:57:~~08 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 23 08:19:33 2009''