2q1d - Revision history

OCA at 11:15, 30 August 2023

OCA — Wed, 30 Aug 2023 11:15:45 GMT

←Older revision		Revision as of 11:15, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2q1d' size='340' side='right'caption='[[2q1d]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2q1d' size='340' side='right'caption='[[2q1d]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2q1d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Sulso Sulso~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q1D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2q1d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q1D FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DO4:2,5~~-~~DIOXOPENTANOIC+ACID'>DO4</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2q18\|2q18]], [[2q19\|2q19]], [[2q1a\|2q1a]], [[2q1c\|2q1c]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DO4:2,5-DIOXOPENTANOIC+ACID'>DO4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">kdaD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])~~</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=2q1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1d OCA], [https://pdbe.org/2q1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q1d RCSB], [https://www.ebi.ac.uk/pdbsum/2q1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1d 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=2q1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1d OCA], [https://pdbe.org/2q1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q1d RCSB], [https://www.ebi.ac.uk/pdbsum/2q1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1d ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/KDAD_SACS2 KDAD_SACS2] Participates in a pentose oxidation pathway that converts D-arabinonate to 2-oxoglutarate.<ref>PMID:16849334</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sulso~~]]	+	[[Category: Saccharolobus solfataricus P2]]
-	[[Category: Akerboom, J]]	+	[[Category: Akerboom J]]
-	[[Category: Barends, T]]	+	[[Category: Barends T]]
-	[[Category: Brouns, S]]	+	[[Category: Brouns S]]
-	[[Category: Salmon, L]]	+	[[Category: Salmon L]]
-	[[Category: Turnbull, A]]	+	[[Category: Turnbull A]]
-	[[Category: Worm, P]]	+	[[Category: Worm P]]
-	~~[[Category: Fah-family fold]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 08:04, 25 June 2021

OCA — Fri, 25 Jun 2021 08:04:59 GMT

←Older revision		Revision as of 08:04, 25 June 2021
Line 1:		Line 1:

	==2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2,5-dioxopentanoate==		==2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2,5-dioxopentanoate==
-	<StructureSection load='2q1d' size='340' side='right' caption='[[2q1d]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='2q1d' size='340' side='right'caption='[[2q1d]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2q1d]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Q1D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2q1d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q1D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DO4:2,5-DIOXOPENTANOIC+ACID'>DO4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DO4:2,5-DIOXOPENTANOIC+ACID'>DO4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2q18\|2q18]], [[2q19\|2q19]], [[2q1a\|2q1a]], [[2q1c\|2q1c]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2q18\|2q18]], [[2q19\|2q19]], [[2q1a\|2q1a]], [[2q1c\|2q1c]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdaD ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdaD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</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=2q1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1d OCA], [~~http~~://pdbe.org/2q1d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2q1d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2q1d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1d 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=2q1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1d OCA], [https://pdbe.org/2q1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q1d RCSB], [https://www.ebi.ac.uk/pdbsum/2q1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1d ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 32:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Sulso]]		[[Category: Sulso]]
	[[Category: Akerboom, J]]		[[Category: Akerboom, J]]

OCA at 08:51, 29 August 2018

OCA — Wed, 29 Aug 2018 08:51:01 GMT

←Older revision		Revision as of 08:51, 29 August 2018
Line 1:		Line 1:
		+
	==2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2,5-dioxopentanoate==		==2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2,5-dioxopentanoate==
	<StructureSection load='2q1d' size='340' side='right' caption='[[2q1d]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2q1d' size='340' side='right' caption='[[2q1d]], [[Resolution\|resolution]] 2.70Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2q18\|2q18]], [[2q19\|2q19]], [[2q1a\|2q1a]], [[2q1c\|2q1c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2q18\|2q18]], [[2q19\|2q19]], [[2q1a\|2q1a]], [[2q1c\|2q1c]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</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=2q1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1d OCA], [http://pdbe.org/2q1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q1d RCSB], [http://www.ebi.ac.uk/pdbsum/2q1d 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=2q1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1d OCA], [http://pdbe.org/2q1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q1d RCSB], [http://www.ebi.ac.uk/pdbsum/2q1d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1d ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q1/2q1d_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q1/2q1d_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>
	</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=2q1d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:10, 11 September 2015

OCA — Fri, 11 Sep 2015 07:10:45 GMT

←Older revision		Revision as of 07:10, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2q1d' size='340' side='right' caption='[[2q1d]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2q1d' size='340' side='right' caption='[[2q1d]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2q1d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sulfolobus_solfataricus Sulfolobus solfataricus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q1D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2q1d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q1D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DO4:2,5-DIOXOPENTANOIC+ACID'>DO4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DO4:2,5-DIOXOPENTANOIC+ACID'>DO4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2q18\|2q18]], [[2q19\|2q19]], [[2q1a\|2q1a]], [[2q1c\|2q1c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2q18\|2q18]], [[2q19\|2q19]], [[2q1a\|2q1a]], [[2q1c\|2q1c]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~2287 Sulfolobus solfataricus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</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=2q1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q1d RCSB], [http://www.ebi.ac.uk/pdbsum/2q1d 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=2q1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1d OCA], [http://pdbe.org/2q1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q1d RCSB], [http://www.ebi.ac.uk/pdbsum/2q1d PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 2q1d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Sulfolobus solfataricus~~]]	+	[[Category: Sulso]]
	[[Category: Akerboom, J]]		[[Category: Akerboom, J]]
	[[Category: Barends, T]]		[[Category: Barends, T]]

OCA at 18:28, 19 January 2015

OCA — Mon, 19 Jan 2015 18:28:41 GMT

←Older revision		Revision as of 18:28, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2q1d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q1D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2q1d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q1D FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DO4:2,5-DIOXOPENTANOIC+ACID'>DO4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DO4:2,5-DIOXOPENTANOIC+ACID'>DO4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2q18\|2q18]], [[2q19\|2q19]], [[2q1a\|2q1a]], [[2q1c\|2q1c]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2q18\|2q18]], [[2q19\|2q19]], [[2q1a\|2q1a]], [[2q1c\|2q1c]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])</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=2q1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q1d RCSB], [http://www.ebi.ac.uk/pdbsum/2q1d 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=2q1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q1d RCSB], [http://www.ebi.ac.uk/pdbsum/2q1d 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: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]
-	[[Category: Akerboom, J.]]	+	[[Category: Akerboom, J]]
-	[[Category: Barends, T.]]	+	[[Category: Barends, T]]
-	[[Category: Brouns, S.]]	+	[[Category: Brouns, S]]
-	[[Category: Salmon, L.]]	+	[[Category: Salmon, L]]
-	[[Category: Turnbull, A.]]	+	[[Category: Turnbull, A]]
-	[[Category: Worm, P.]]	+	[[Category: Worm, P]]
	[[Category: Fah-family fold]]		[[Category: Fah-family fold]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 20:15, 30 September 2014

OCA — Tue, 30 Sep 2014 20:15:05 GMT

←Older revision		Revision as of 20:15, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2q1d.~~png~~\|~~left~~\|200px]]	+	==2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2,5-dioxopentanoate==
		+	<StructureSection load='2q1d' size='340' side='right' caption='[[2q1d]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2q1d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q1D FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DO4:2,5-DIOXOPENTANOIC+ACID'>DO4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2q18\|2q18]], [[2q19\|2q19]], [[2q1a\|2q1a]], [[2q1c\|2q1c]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])</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=2q1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q1d RCSB], [http://www.ebi.ac.uk/pdbsum/2q1d 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/q1/2q1d_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 archaeon Sulfolobus solfataricus converts d-arabinose to 2-oxoglutarate by an enzyme set consisting of two dehydrogenases and two dehydratases. The third step of the pathway is catalyzed by a novel 2-keto-3-deoxy-D-arabinonate dehydratase (KdaD). In this study, the crystal structure of the enzyme has been solved to 2.1 A resolution. The enzyme forms an oval-shaped ring of four subunits, each consisting of an N-terminal domain with a four-stranded beta-sheet flanked by two alpha-helices, and a C-terminal catalytic domain with a fumarylacetoacetate hydrolase (FAH) fold. Crystal structures of complexes of the enzyme with magnesium or calcium ions and either a substrate analog 2-oxobutyrate, or the aldehyde enzyme product 2,5-dioxopentanoate revealed that the divalent metal ion in the active site is coordinated octahedrally by three conserved carboxylate residues, a water molecule, and both the carboxylate and the oxo groups of the substrate molecule. An enzymatic mechanism for base-catalyzed dehydration is proposed on the basis of the binding mode of the substrate to the metal ion, which suggests that the enzyme enhances the acidity of the protons alpha to the carbonyl group, facilitating their abstraction by glutamate 114. A comprehensive structural comparison of members of the FAH superfamily is presented and their evolution is discussed, providing a basis for functional investigations of this largely unexplored protein superfamily.

-	~~{{STRUCTURE_2q1d\| PDB=2q1d \| SCENE= }}~~	+	Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily.,Brouns SJ, Barends TR, Worm P, Akerboom J, Turnbull AP, Salmon L, van der Oost J J Mol Biol. 2008 May 30;379(2):357-71. Epub 2008 Apr 8. PMID:18448118<ref>PMID:18448118</ref>

-	~~===2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2~~,~~5-dioxopentanoate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18448118}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2q1d]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018448118<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Sulfolobus solfataricus]]		[[Category: Sulfolobus solfataricus]]
	[[Category: Akerboom, J.]]		[[Category: Akerboom, J.]]

OCA: Protected "2q1d" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 20:23:34 GMT

Protected "2q1d" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:23, 7 January 2013

OCA at 20:23, 7 January 2013

OCA — Mon, 07 Jan 2013 20:23:31 GMT

←Older revision		Revision as of 20:23, 7 January 2013
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-	{{Seed}}
	[[Image:2q1d.png\|left\|200px]]		[[Image:2q1d.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2q1d", 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),
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	{{STRUCTURE_2q1d\| PDB=2q1d \| SCENE= }}		{{STRUCTURE_2q1d\| PDB=2q1d \| SCENE= }}

	===2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2,5-dioxopentanoate===		===2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2,5-dioxopentanoate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18448118}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18448118 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_18448118}}		{{ABSTRACT_PUBMED_18448118}}

	==About this Structure==		==About this Structure==
-	~~2Q1D~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/~~Sulfolobus_solfataricus_p2~~ Sulfolobus solfataricus p2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA].	+	[[2q1d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18448118~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018448118</ref><references group="xtra"/>
-	[[Category: Sulfolobus solfataricus p2]]	+	[[Category: Sulfolobus solfataricus]]
	[[Category: Akerboom, J.]]		[[Category: Akerboom, J.]]
	[[Category: Barends, T.]]		[[Category: Barends, T.]]
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	[[Category: Fah-family fold]]		[[Category: Fah-family fold]]
	[[Category: Lyase]]		[[Category: Lyase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:54:06 2009''

OCA at 14:54, 17 February 2009

OCA — Tue, 17 Feb 2009 14:54:07 GMT

←Older revision		Revision as of 14:54, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2Q1D is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus_p2 Sulfolobus solfataricus p2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA].	+	2Q1D is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus_p2 Sulfolobus solfataricus p2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA].

	==Reference==		==Reference==
-	Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily., Brouns SJ, Barends TR, Worm P, Akerboom J, Turnbull AP, Salmon L, van der Oost J, J Mol Biol. 2008 May 30;379(2):357-71. Epub 2008 Apr 8. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18448118 18448118]~~	+	<ref group="xtra">PMID:18448118</ref><references group="xtra"/>
-	~~[[Category: Single protein]]~~	+
	[[Category: Sulfolobus solfataricus p2]]		[[Category: Sulfolobus solfataricus p2]]
	[[Category: Akerboom, J.]]		[[Category: Akerboom, J.]]
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	[[Category: Lyase]]		[[Category: Lyase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 2 21~~:25:~~32 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:54:06 2009''

OCA at 18:25, 2 July 2008

OCA — Wed, 02 Jul 2008 18:25:32 GMT

←Older revision		Revision as of 18:25, 2 July 2008
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-	[[Image:2q1d.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2q1d.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2q1d\| PDB=2q1d \| SCENE= }}		{{STRUCTURE_2q1d\| PDB=2q1d \| SCENE= }}

-	~~'''~~2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2,5-dioxopentanoate~~'''~~	+	===2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2,5-dioxopentanoate===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_18448118}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18448118 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18448118}}

	==About this Structure==		==About this Structure==
-	2Q1D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/~~Sulfolobus_solfataricus~~ Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA].	+	2Q1D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus_p2 Sulfolobus solfataricus p2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA].
		+
		+	==Reference==
		+	Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily., Brouns SJ, Barends TR, Worm P, Akerboom J, Turnbull AP, Salmon L, van der Oost J, J Mol Biol. 2008 May 30;379(2):357-71. Epub 2008 Apr 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18448118 18448118]
	[[Category: Single protein]]		[[Category: Single protein]]
-	[[Category: Sulfolobus solfataricus]]	+	[[Category: Sulfolobus solfataricus p2]]
	[[Category: Akerboom, J.]]		[[Category: Akerboom, J.]]
	[[Category: Barends, T.]]		[[Category: Barends, T.]]
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	[[Category: Fah-family fold]]		[[Category: Fah-family fold]]
	[[Category: Lyase]]		[[Category: Lyase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 21:25:32 2008''