3dds - Revision history

OCA at 12:45, 30 August 2023

2023-08-30T12:45:43Z

← Older revision		Revision as of 12:45, 30 August 2023
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	<StructureSection load='3dds' size='340' side='right'caption='[[3dds]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3dds' size='340' side='right'caption='[[3dds]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dds]] 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=3DDS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDS FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dds]] 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=3DDS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=26B:O-TERT-BUTYL-N-[(3-{[(2,4,6-TRIMETHYLPHENYL)CARBAMOYL]AMINO}NAPHTHALEN-2-YL)CARBONYL]-L-THREONINE'>26B</scene>, <scene name='pdbligand=CFF:CAFFEINE'>CFF</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NBG:1-N-ACETYL-BETA-D-GLUCOSAMINE'>NBG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.8Å</td></tr>
	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene~~></td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=26B:O-TERT-BUTYL-N-[(3-{[(2,4,6-TRIMETHYLPHENYL)CARBAMOYL]AMINO}NAPHTHALEN-2-YL)CARBONYL]-L-THREONINE'>26B</scene>, <scene name='pdbligand=CFF:CAFFEINE'>CFF</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NBG:1-N-ACETYL-BETA-D-GLUCOSAMINE'>NBG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dd1\|3dd1]], [[3ddw\|3ddw]]</div></td></tr>~~
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYGL ([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/Phosphorylase Phosphorylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] </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=3dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dds OCA], [https://pdbe.org/3dds PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dds RCSB], [https://www.ebi.ac.uk/pdbsum/3dds PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dds 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=3dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dds OCA], [https://pdbe.org/3dds PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dds RCSB], [https://www.ebi.ac.uk/pdbsum/3dds PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dds ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
	[[https://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN]] Defects in PYGL are the cause of glycogen storage disease type 6 (GSD6) [MIM:[https://omim.org/entry/232700 232700]]. A metabolic disorder characterized by mild to moderate hypoglycemia, mild ketosis, growth retardation, and prominent hepatomegaly. Heart and skeletal muscle are not affected.<ref>PMID:9529348</ref>		[https://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN] Defects in PYGL are the cause of glycogen storage disease type 6 (GSD6) [MIM:[https://omim.org/entry/232700 232700]. A metabolic disorder characterized by mild to moderate hypoglycemia, mild ketosis, growth retardation, and prominent hepatomegaly. Heart and skeletal muscle are not affected.<ref>PMID:9529348</ref>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN]] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.		[https://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.
	== 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: Phosphorylase]]~~		[[Category: Nolte RT]]
	[[Category: Nolte~~, R T]]~~
	~~[[Category: Allosteric enzyme]]~~
	~~[[Category: Carbohydrate metabolism]]~~
	~~[[Category: Diabetes]]~~
	~~[[Category: Disease mutation]]~~
	~~[[Category: Glycogen metabolism]]~~
	~~[[Category: Glycogen phosphorylase]]~~
	~~[[Category: Glycogen storage disease]]~~
	~~[[Category: Glycosyltransferase]]~~
	~~[[Category: Gp]]~~
	~~[[Category: Nucleotide-binding]]~~
	~~[[Category: Phosphoprotein]]~~
	~~[[Category: Pyridoxal phosphate]]~~
	~~[[Category: Transferase~~]]

OCA at 07:56, 9 February 2022

2022-02-09T07:56:37Z

← Older revision		Revision as of 07:56, 9 February 2022
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	==Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK261==		==Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK261==
	<StructureSection load='3dds' size='340' side='right' caption='[[3dds]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3dds' size='340' side='right'caption='[[3dds]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dds]] 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=3DDS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DDS FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dds]] 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=3DDS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=26B:O-TERT-BUTYL-N-[(3-{[(2,4,6-TRIMETHYLPHENYL)CARBAMOYL]AMINO}NAPHTHALEN-2-YL)CARBONYL]-L-THREONINE'>26B</scene>, <scene name='pdbligand=CFF:CAFFEINE'>CFF</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NBG:1-N-ACETYL-BETA-D-GLUCOSAMINE'>NBG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=26B:O-TERT-BUTYL-N-[(3-{[(2,4,6-TRIMETHYLPHENYL)CARBAMOYL]AMINO}NAPHTHALEN-2-YL)CARBONYL]-L-THREONINE'>26B</scene>, <scene name='pdbligand=CFF:CAFFEINE'>CFF</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NBG:1-N-ACETYL-BETA-D-GLUCOSAMINE'>NBG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dd1\|3dd1]], [[3ddw\|3ddw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dd1\|3dd1]], [[3ddw\|3ddw]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYGL ([~~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">PYGL ([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/Phosphorylase Phosphorylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphorylase Phosphorylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] </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=3dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dds OCA], [~~http~~://pdbe.org/3dds PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dds RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dds PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dds 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=3dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dds OCA], [https://pdbe.org/3dds PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dds RCSB], [https://www.ebi.ac.uk/pdbsum/3dds PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dds ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
	[[~~http~~://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN]] Defects in PYGL are the cause of glycogen storage disease type 6 (GSD6) [MIM:[~~http~~://omim.org/entry/232700 232700]]. A metabolic disorder characterized by mild to moderate hypoglycemia, mild ketosis, growth retardation, and prominent hepatomegaly. Heart and skeletal muscle are not affected.<ref>PMID:9529348</ref>		[[https://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN]] Defects in PYGL are the cause of glycogen storage disease type 6 (GSD6) [MIM:[https://omim.org/entry/232700 232700]]. A metabolic disorder characterized by mild to moderate hypoglycemia, mild ketosis, growth retardation, and prominent hepatomegaly. Heart and skeletal muscle are not affected.<ref>PMID:9529348</ref>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN]] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.		[[https://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN]] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
	*[[Glycogen ~~Phosphorylase~~\|Glycogen ~~Phosphorylase~~]]		*[[Glycogen phosphorylase 3D structures\|Glycogen phosphorylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Phosphorylase]]		[[Category: Phosphorylase]]
	[[Category: Nolte, R T]]		[[Category: Nolte, R T]]

OCA at 09:52, 14 November 2018

2018-11-14T09:52:45Z

← Older revision		Revision as of 09:52, 14 November 2018
Line 1:		Line 1:

	==Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK261==		==Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK261==
	<StructureSection load='3dds' size='340' side='right' caption='[[3dds]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3dds' size='340' side='right' caption='[[3dds]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYGL ([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">PYGL ([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/Phosphorylase Phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphorylase Phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] </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=3dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dds OCA], [http://pdbe.org/3dds PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dds RCSB], [http://www.ebi.ac.uk/pdbsum/3dds 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=3dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dds OCA], [http://pdbe.org/3dds PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dds RCSB], [http://www.ebi.ac.uk/pdbsum/3dds PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dds ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 18:		Line 19:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/3dds_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/3dds_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 10:08, 8 February 2016

2016-02-08T10:08:33Z

← Older revision		Revision as of 10:08, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3dds' size='340' side='right' caption='[[3dds]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='3dds' size='340' side='right' caption='[[3dds]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dds]] 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=3DDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DDS FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dds]] 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=3DDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DDS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=26B:O-TERT-BUTYL-N-[(3-{[(2,4,6-TRIMETHYLPHENYL)CARBAMOYL]AMINO}NAPHTHALEN-2-YL)CARBONYL]-L-THREONINE'>26B</scene>, <scene name='pdbligand=CFF:CAFFEINE'>CFF</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NBG:1-N-ACETYL-BETA-D-GLUCOSAMINE'>NBG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=26B:O-TERT-BUTYL-N-[(3-{[(2,4,6-TRIMETHYLPHENYL)CARBAMOYL]AMINO}NAPHTHALEN-2-YL)CARBONYL]-L-THREONINE'>26B</scene>, <scene name='pdbligand=CFF:CAFFEINE'>CFF</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NBG:1-N-ACETYL-BETA-D-GLUCOSAMINE'>NBG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dd1\|3dd1]], [[3ddw\|3ddw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dd1\|3dd1]], [[3ddw\|3ddw]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYGL ([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">PYGL ([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/Phosphorylase Phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphorylase Phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] </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=3dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dds OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dds RCSB], [http://www.ebi.ac.uk/pdbsum/3dds 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=3dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dds OCA], [http://pdbe.org/3dds PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dds RCSB], [http://www.ebi.ac.uk/pdbsum/3dds PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 22:		Line 22:
	<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=3dds ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 32:		Line 32:
	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 3dds" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 39:		Line 40:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Phosphorylase]]		[[Category: Phosphorylase]]
	[[Category: Nolte, R T]]		[[Category: Nolte, R T]]

OCA at 14:14, 18 December 2014

2014-12-18T14:14:09Z

← Older revision		Revision as of 14:14, 18 December 2014
Line 1:		Line 1:
	~~{{STRUCTURE_3dds\| PDB=3dds \| SCENE= }}~~		==Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK261==
	===Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK261===		<StructureSection load='3dds' size='340' side='right' caption='[[3dds]], [[Resolution\|resolution]] 1.80Å' scene=''>
	{~~{ABSTRACT_PUBMED_19138846}~~}		== Structural highlights ==
			<table><tr><td colspan='2'>[[3dds]] 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=3DDS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DDS FirstGlance]. <br>
	==Disease==		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=26B:O-TERT-BUTYL-N-[(3-{[(2,4,6-TRIMETHYLPHENYL)CARBAMOYL]AMINO}NAPHTHALEN-2-YL)CARBONYL]-L-THREONINE'>26B</scene>, <scene name='pdbligand=CFF:CAFFEINE'>CFF</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NBG:1-N-ACETYL-BETA-D-GLUCOSAMINE'>NBG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	[[http://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN]] Defects in PYGL are the cause of glycogen storage disease type 6 (GSD6) [MIM:[http://omim.org/entry/232700 232700]]. A metabolic disorder characterized by mild to moderate hypoglycemia, mild ketosis, growth retardation, and prominent hepatomegaly. Heart and skeletal muscle are not affected.<ref>PMID:9529348</ref>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dd1\|3dd1]], [[3ddw\|3ddw]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PYGL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphorylase Phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] </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=3dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dds OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dds RCSB], [http://www.ebi.ac.uk/pdbsum/3dds PDBsum]</span></td></tr>
			</table>
			== Disease ==
			[[http://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN]] Defects in PYGL are the cause of glycogen storage disease type 6 (GSD6) [MIM:[http://omim.org/entry/232700 232700]]. A metabolic disorder characterized by mild to moderate hypoglycemia, mild ketosis, growth retardation, and prominent hepatomegaly. Heart and skeletal muscle are not affected.<ref>PMID:9529348</ref>
			== Function ==
			[[http://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN]] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.
			== 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/dd/3dds_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 ==
			Key binding interactions of the anthranilimide based glycogen phosphorylase a (GPa) inhibitor 2 from X-ray crystallography studies are described. This series of compounds bind to the AMP site of GP. Using the binding information the core and the phenyl urea moieties were optimized. This work culminated in the identification of compounds with single nanomolar potency as well as in vivo efficacy in a diabetic model.

	~~==Function==~~		Anthranilimide based glycogen phosphorylase inhibitors for the treatment of type 2 diabetes. Part 3: X-ray crystallographic characterization, core and urea optimization and in vivo efficacy.,Thomson SA, Banker P, Bickett DM, Boucheron JA, Carter HL, Clancy DC, Cooper JP, Dickerson SH, Garrido DM, Nolte RT, Peat AJ, Sheckler LR, Sparks SM, Tavares FX, Wang L, Wang TY, Weiel JE Bioorg Med Chem Lett. 2009 Feb 15;19(4):1177-82. Epub 2008 Dec 25. PMID:19138846<ref>PMID:19138846</ref>
	~~[[http~~:~~//www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN]] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms~~ and in ~~their natural substrates~~. ~~However~~, ~~all known phosphorylases share catalytic and structural properties~~.

	~~==About this Structure==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[3dds]] 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=3DDS OCA].~~		</div>

	==See Also==		==See Also==
	*[[Glycogen Phosphorylase\|Glycogen Phosphorylase]]		*[[Glycogen Phosphorylase\|Glycogen Phosphorylase]]
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:019138846</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
			</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Phosphorylase]]		[[Category: Phosphorylase]]
	[[Category: Nolte, R T.]]		[[Category: Nolte, R T]]
	[[Category: Allosteric enzyme]]		[[Category: Allosteric enzyme]]
	[[Category: Carbohydrate metabolism]]		[[Category: Carbohydrate metabolism]]

OCA at 10:16, 24 March 2013

2013-03-24T10:16:30Z

← Older revision		Revision as of 10:16, 24 March 2013
Line 1:		Line 1:
	~~[[Image:3dds.png\|left\|200px]]~~

	{{STRUCTURE_3dds\| PDB=3dds \| SCENE= }}		{{STRUCTURE_3dds\| PDB=3dds \| SCENE= }}
			===Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK261===
			{{ABSTRACT_PUBMED_19138846}}

	===~~Crystal structure~~ of glycogen ~~phosphorylase complexed with an anthranilimide based inhibitor GSK261===~~		==Disease==
			[[http://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN]] Defects in PYGL are the cause of glycogen storage disease type 6 (GSD6) [MIM:[http://omim.org/entry/232700 232700]]. A metabolic disorder characterized by mild to moderate hypoglycemia, mild ketosis, growth retardation, and prominent hepatomegaly. Heart and skeletal muscle are not affected.<ref>PMID:9529348</ref>

	~~{{ABSTRACT_PUBMED_19138846}}~~		==Function==
			[[http://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN]] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.

	==About this Structure==		==About this Structure==
Line 14:		Line 16:

	==Reference==		==Reference==
	<ref group="xtra">PMID:019138846</ref><references group="xtra"/>		<ref group="xtra">PMID:019138846</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Phosphorylase]]		[[Category: Phosphorylase]]

OCA at 09:48, 20 October 2012

2012-10-20T09:48:38Z

← Older revision		Revision as of 09:48, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[3dds]] is a 2 chain structure ~~of [[Glycogen Phosphorylase]]~~ 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=3DDS OCA].		[[3dds]] 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=3DDS OCA].

	==See Also==		==See Also==

OCA: Protected "3dds" [edit=sysop:move=sysop]

2012-07-26T00:01:42Z

Protected "3dds" [edit=sysop:move=sysop]

← Older revision	Revision as of 00:01, 26 July 2012
(No difference)

OCA at 00:01, 26 July 2012

2012-07-26T00:01:41Z

← Older revision		Revision as of 00:01, 26 July 2012
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:3dds.png\|left\|200px]]		[[Image:3dds.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3dds", 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_3dds\| PDB=3dds \| SCENE= }}		{{STRUCTURE_3dds\| PDB=3dds \| SCENE= }}

	===Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK261===		===Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK261===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_19138846}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 19138846 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_19138846}}		{{ABSTRACT_PUBMED_19138846}}

	==About this Structure==		==About this Structure==
	~~3DDS~~ is a 2 ~~chains~~ structure with ~~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=3DDS OCA].		[[3dds]] is a 2 chain structure of [[Glycogen Phosphorylase]] 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=3DDS OCA].

			==See Also==
			*[[Glycogen Phosphorylase\|Glycogen Phosphorylase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~19138846~~</ref><references group="xtra"/>		<ref group="xtra">PMID:019138846</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Phosphorylase]]		[[Category: Phosphorylase]]
	[[Category: Nolte, R T.]]		[[Category: Nolte, R T.]]
	~~[[Category: Acetylation]]~~
	[[Category: Allosteric enzyme]]		[[Category: Allosteric enzyme]]
	[[Category: Carbohydrate metabolism]]		[[Category: Carbohydrate metabolism]]
Line 39:		Line 29:
	[[Category: Nucleotide-binding]]		[[Category: Nucleotide-binding]]
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
	~~[[Category: Polymorphism]]~~
	[[Category: Pyridoxal phosphate]]		[[Category: Pyridoxal phosphate]]
	[[Category: Transferase]]		[[Category: Transferase]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:59:22 2010''~~

OCA at 08:50, 22 September 2010

2010-09-22T08:50:24Z

← Older revision		Revision as of 08:50, 22 September 2010
Line 18:		Line 18:
	-->		-->
	{{ABSTRACT_PUBMED_19138846}}		{{ABSTRACT_PUBMED_19138846}}

	~~==Disease==~~
	~~Known disease associated with this structure: Glycogen storage disease VI OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=232700 232700]]~~

	==About this Structure==		==About this Structure==
	3DDS is a ~~[[Single protein]]~~ structure ~~of 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=3DDS OCA].		3DDS is a 2 chains structure with 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=3DDS OCA].

	==Reference==		==Reference==
	Anthranilimide based glycogen phosphorylase inhibitors for the treatment of type 2 diabetes. Part 3: X-ray crystallographic characterization, core and urea optimization and in vivo efficacy., Thomson SA, Banker P, Bickett DM, Boucheron JA, Carter HL, Clancy DC, Cooper JP, Dickerson SH, Garrido DM, Nolte RT, Peat AJ, Sheckler LR, Sparks SM, Tavares FX, Wang L, Wang TY, Weiel JE, Bioorg Med Chem Lett. 2008 Dec 25. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/19138846 19138846]~~		<ref group="xtra">PMID:19138846</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Phosphorylase]]		[[Category: Phosphorylase]]
	[[Category: ~~Single protein]]~~		[[Category: Nolte, R T.]]
	~~[[Category: Pdbx_ordinal=~~, ~~<PDBx:audit_author~~.]]
	[[Category: Acetylation]]		[[Category: Acetylation]]
	[[Category: Allosteric enzyme]]		[[Category: Allosteric enzyme]]
Line 47:		Line 43:
	[[Category: Transferase]]		[[Category: Transferase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 4 20~~:12:~~24 2009~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:59:22 2010''