1ihy - Revision history

OCA at 13:24, 13 March 2024

OCA — Wed, 13 Mar 2024 13:24:19 GMT

←Older revision		Revision as of 13:24, 13 March 2024
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	<StructureSection load='1ihy' size='340' side='right'caption='[[1ihy]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1ihy' size='340' side='right'caption='[[1ihy]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ihy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Palinurus_versicolor Palinurus~~ versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IHY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ihy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Panulirus_versicolor Panulirus versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IHY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=APR:ADENOSINE~~-~~5-DIPHOSPHORIBOSE'>APR</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 3Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1ihx\|1ihx]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] </~~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=1ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ihy OCA], [https://pdbe.org/1ihy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ihy RCSB], [https://www.ebi.ac.uk/pdbsum/1ihy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ihy 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=1ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ihy OCA], [https://pdbe.org/1ihy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ihy RCSB], [https://www.ebi.ac.uk/pdbsum/1ihy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ihy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G3P_PANVR G3P_PANVR]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1ihy 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=1ihy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Crystal structures of GAPDH from Palinurus versicolor complexed with two coenzyme analogues, SNAD(+) and ADP-ribose, were determined by molecular replacement and refined at medium resolution to acceptable crystallographic factors and reasonable stereochemistry. ADP-ribose in the ADP-ribose-GAPDH complex adopts a rather extended conformation. The interactions between ADP-ribose and GAPDH are extensive and in a fashion dissimilar to the coenzyme NAD(+). This accounts for the strong inhibiting ability of ADP-ribose. The conformational changes induced by ADP-ribose binding are quite different to those induced by NAD(+) binding. This presumably explains the non-cooperative behaviour of the ADP-ribose binding. Unexpectedly, the SNAD(+)-GAPDH complex reveals pairwise asymmetry. The asymmetry is significant, including the SNAD(+) molecule, active-site structure and domain motion induced by the coenzyme analogue. In the yellow or red subunits [nomenclature of subunits is as in Buehner et al. (1974). J. Mol. Biol. 90, 25-49], SNAD(+) binds similarly, as does NAD(+) in holo-GAPDH. While, in the green or blue subunit, the SNAD(+) binds in a non-productive manner, resulting in a disordered thionicotinamide ring and rearranged active-site residues. The conformation seen in the yellow and red subunits of SNAD(+)-GAPDH is likely to represent the functional state of the enzyme complex in solution and thus accounts for the substrate activity of SNAD(+). A novel type of domain motion is observed for the binding of the coenzyme analogues to GAPDH. The possible conformational transitions involved in the coenzyme binding and the important role of the nicotinamide group are discussed.
-
-	Structures of D-glyceraldehyde-3-phosphate dehydrogenase complexed with coenzyme analogues.,Shen YQ, Song SY, Lin ZJ Acta Crystallogr D Biol Crystallogr. 2002 Aug;58(Pt 8):1287-97. Epub 2002, Jul 20. PMID:12136140<ref>PMID:12136140</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ihy" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Aldehyde dehydrogenase 3D structures\|Aldehyde dehydrogenase 3D structures]]		*[[Aldehyde dehydrogenase 3D structures\|Aldehyde dehydrogenase 3D structures]]
	*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures\|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]		*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures\|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Palinurus~~ versicolor]]	+	[[Category: Panulirus versicolor]]
-	[[Category: Lin, Z J]]	+	[[Category: Lin Z-J]]
-	[[Category: Shen, Y Q]]	+	[[Category: Shen Y-Q]]
-	[[Category: Song, S Y]]	+	[[Category: Song S-Y]]
-	~~[[Category: Adp-ribose]]~~	+
-	~~[[Category: D-glyceraldehyde-3-phosphate dehydrogenase]]~~	+
-	~~[[Category: Gapdh]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:43, 7 April 2021

OCA — Wed, 07 Apr 2021 07:43:06 GMT

←Older revision		Revision as of 07:43, 7 April 2021
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	<StructureSection load='1ihy' size='340' side='right'caption='[[1ihy]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1ihy' size='340' side='right'caption='[[1ihy]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ihy]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Palinurus_versicolor Palinurus versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1IHY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ihy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Palinurus_versicolor Palinurus versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IHY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ihx\|1ihx]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ihx\|1ihx]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] </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=1ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ihy OCA], [~~http~~://pdbe.org/1ihy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ihy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ihy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ihy 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=1ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ihy OCA], [https://pdbe.org/1ihy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ihy RCSB], [https://www.ebi.ac.uk/pdbsum/1ihy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ihy ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	==See Also==		==See Also==
	*[[Aldehyde dehydrogenase 3D structures\|Aldehyde dehydrogenase 3D structures]]		*[[Aldehyde dehydrogenase 3D structures\|Aldehyde dehydrogenase 3D structures]]
-	*[[Glyceraldehyde-3-~~Phosphate Dehydrogenase~~\|Glyceraldehyde-3-~~Phosphate Dehydrogenase~~]]	+	*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures\|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:28, 3 July 2019

OCA — Wed, 03 Jul 2019 07:28:05 GMT

←Older revision		Revision as of 07:28, 3 July 2019
Line 1:		Line 1:

	==GAPDH complexed with ADP-ribose==		==GAPDH complexed with ADP-ribose==
-	<StructureSection load='1ihy' size='340' side='right' caption='[[1ihy]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='1ihy' size='340' side='right'caption='[[1ihy]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ihy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Palinurus_versicolor Palinurus versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IHY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ihy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Palinurus_versicolor Palinurus versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IHY FirstGlance]. <br>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ih/1ihy_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ih/1ihy_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>
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Aldehyde dehydrogenase\|Aldehyde dehydrogenase]]	+	*[[Aldehyde dehydrogenase 3D structures\|Aldehyde dehydrogenase 3D structures]]
		+	*[[Glyceraldehyde-3-Phosphate Dehydrogenase\|Glyceraldehyde-3-Phosphate Dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Palinurus versicolor]]		[[Category: Palinurus versicolor]]
	[[Category: Lin, Z J]]		[[Category: Lin, Z J]]

OCA at 10:52, 27 September 2017

OCA — Wed, 27 Sep 2017 10:52:21 GMT

←Older revision		Revision as of 10:52, 27 September 2017
Line 1:		Line 1:
		+
	==GAPDH complexed with ADP-ribose==		==GAPDH complexed with ADP-ribose==
	<StructureSection load='1ihy' size='340' side='right' caption='[[1ihy]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1ihy' size='340' side='right' caption='[[1ihy]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ihy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Panulirus_versicolor Panulirus~~ versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IHY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ihy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Palinurus_versicolor Palinurus versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IHY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ihx\|1ihx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ihx\|1ihx]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] </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=1ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ihy OCA], [http://pdbe.org/1ihy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ihy RCSB], [http://www.ebi.ac.uk/pdbsum/1ihy 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=1ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ihy OCA], [http://pdbe.org/1ihy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ihy RCSB], [http://www.ebi.ac.uk/pdbsum/1ihy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ihy ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<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=1ihy 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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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Panulirus~~ versicolor]]	+	[[Category: Palinurus versicolor]]
	[[Category: Lin, Z J]]		[[Category: Lin, Z J]]
	[[Category: Shen, Y Q]]		[[Category: Shen, Y Q]]

OCA at 09:12, 11 September 2015

OCA — Fri, 11 Sep 2015 09:12:47 GMT

←Older revision		Revision as of 09:12, 11 September 2015
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ihx\|1ihx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ihx\|1ihx]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] </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=1ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ihy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ihy RCSB], [http://www.ebi.ac.uk/pdbsum/1ihy 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=1ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ihy OCA], [http://pdbe.org/1ihy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ihy RCSB], [http://www.ebi.ac.uk/pdbsum/1ihy PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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 1ihy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aldehyde dehydrogenase\|Aldehyde dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:23, 2 January 2015

OCA — Fri, 02 Jan 2015 12:23:18 GMT

←Older revision		Revision as of 12:23, 2 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ihy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Panulirus_versicolor Panulirus versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IHY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ihy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Panulirus_versicolor Panulirus versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IHY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ihx\|1ihx]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ihx\|1ihx]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] </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=1ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ihy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ihy RCSB], [http://www.ebi.ac.uk/pdbsum/1ihy 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=1ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ihy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ihy RCSB], [http://www.ebi.ac.uk/pdbsum/1ihy PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Panulirus versicolor]]		[[Category: Panulirus versicolor]]
-	[[Category: Lin, Z J.]]	+	[[Category: Lin, Z J]]
-	[[Category: Shen, Y Q.]]	+	[[Category: Shen, Y Q]]
-	[[Category: Song, S Y.]]	+	[[Category: Song, S Y]]
	[[Category: Adp-ribose]]		[[Category: Adp-ribose]]
	[[Category: D-glyceraldehyde-3-phosphate dehydrogenase]]		[[Category: D-glyceraldehyde-3-phosphate dehydrogenase]]
	[[Category: Gapdh]]		[[Category: Gapdh]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 11:11, 3 October 2014

OCA — Fri, 03 Oct 2014 11:11:09 GMT

←Older revision		Revision as of 11:11, 3 October 2014
Line 1:		Line 1:
-	[[~~Image:~~1ihy.~~png~~\|~~left~~\|200px]]	+	==GAPDH complexed with ADP-ribose==
		+	<StructureSection load='1ihy' size='340' side='right' caption='[[1ihy]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ihy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Panulirus_versicolor Panulirus versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IHY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ihx\|1ihx]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] </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=1ihy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ihy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ihy RCSB], [http://www.ebi.ac.uk/pdbsum/1ihy 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/ih/1ihy_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 ==
		+	Crystal structures of GAPDH from Palinurus versicolor complexed with two coenzyme analogues, SNAD(+) and ADP-ribose, were determined by molecular replacement and refined at medium resolution to acceptable crystallographic factors and reasonable stereochemistry. ADP-ribose in the ADP-ribose-GAPDH complex adopts a rather extended conformation. The interactions between ADP-ribose and GAPDH are extensive and in a fashion dissimilar to the coenzyme NAD(+). This accounts for the strong inhibiting ability of ADP-ribose. The conformational changes induced by ADP-ribose binding are quite different to those induced by NAD(+) binding. This presumably explains the non-cooperative behaviour of the ADP-ribose binding. Unexpectedly, the SNAD(+)-GAPDH complex reveals pairwise asymmetry. The asymmetry is significant, including the SNAD(+) molecule, active-site structure and domain motion induced by the coenzyme analogue. In the yellow or red subunits [nomenclature of subunits is as in Buehner et al. (1974). J. Mol. Biol. 90, 25-49], SNAD(+) binds similarly, as does NAD(+) in holo-GAPDH. While, in the green or blue subunit, the SNAD(+) binds in a non-productive manner, resulting in a disordered thionicotinamide ring and rearranged active-site residues. The conformation seen in the yellow and red subunits of SNAD(+)-GAPDH is likely to represent the functional state of the enzyme complex in solution and thus accounts for the substrate activity of SNAD(+). A novel type of domain motion is observed for the binding of the coenzyme analogues to GAPDH. The possible conformational transitions involved in the coenzyme binding and the important role of the nicotinamide group are discussed.

-	~~{{STRUCTURE_1ihy\| PDB=1ihy \| SCENE= }}~~	+	Structures of D-glyceraldehyde-3-phosphate dehydrogenase complexed with coenzyme analogues.,Shen YQ, Song SY, Lin ZJ Acta Crystallogr D Biol Crystallogr. 2002 Aug;58(Pt 8):1287-97. Epub 2002, Jul 20. PMID:12136140<ref>PMID:12136140</ref>

-	~~===GAPDH complexed with ADP-ribose===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12136140}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1ihy]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Panulirus_versicolor Panulirus versicolor]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA].~~	+	</StructureSection>
-		+
-	==~~See Also==~~	+
-	*[[Aldehyde dehydrogenase\|Aldehyde dehydrogenase]]	+
-		+
-	~~==Reference~~==	+
-	<~~ref group="xtra">PMID:012136140<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Panulirus versicolor]]		[[Category: Panulirus versicolor]]
	[[Category: Lin, Z J.]]		[[Category: Lin, Z J.]]

OCA at 17:44, 20 October 2012

OCA — Sat, 20 Oct 2012 17:44:52 GMT

←Older revision		Revision as of 17:44, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1ihy]] is a 4 chain structure ~~of [[Aldehyde dehydrogenase]]~~ with sequence from [http://en.wikipedia.org/wiki/Panulirus_versicolor Panulirus versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA].	+	[[1ihy]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Panulirus_versicolor Panulirus versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA].

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

OCA: Protected "1ihy" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 01:51:59 GMT

Protected "1ihy" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:51, 27 July 2012

OCA at 01:51, 27 July 2012

OCA — Fri, 27 Jul 2012 01:51:57 GMT

←Older revision		Revision as of 01:51, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1ihy.png\|left\|200px]]		[[Image:1ihy.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1ihy", 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_1ihy\| PDB=1ihy \| SCENE= }}		{{STRUCTURE_1ihy\| PDB=1ihy \| SCENE= }}

	===GAPDH complexed with ADP-ribose===		===GAPDH complexed with ADP-ribose===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12136140}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12136140 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12136140}}		{{ABSTRACT_PUBMED_12136140}}

	==About this Structure==		==About this Structure==
-	~~1IHY~~ is a 4 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/~~Palinurus_versicolor Palinurus~~ versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA].	+	[[1ihy]] is a 4 chain structure of [[Aldehyde dehydrogenase]] with sequence from [http://en.wikipedia.org/wiki/Panulirus_versicolor Panulirus versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHY OCA].
		+
		+	==See Also==
		+	*[[Aldehyde dehydrogenase\|Aldehyde dehydrogenase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12136140~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012136140</ref><references group="xtra"/>
-	[[Category: ~~Palinurus~~ versicolor]]	+	[[Category: Panulirus versicolor]]
	[[Category: Lin, Z J.]]		[[Category: Lin, Z J.]]
	[[Category: Shen, Y Q.]]		[[Category: Shen, Y Q.]]
Line 31:		Line 22:
	[[Category: D-glyceraldehyde-3-phosphate dehydrogenase]]		[[Category: D-glyceraldehyde-3-phosphate dehydrogenase]]
	[[Category: Gapdh]]		[[Category: Gapdh]]
-		+	[[Category: Oxidoreductase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 18:32:31 2009''~~	+