3i9m - Revision history

OCA at 15:56, 1 November 2023

2023-11-01T15:56:40Z

←Older revision		Revision as of 15:56, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='3i9m' size='340' side='right'caption='[[3i9m]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='3i9m' size='340' side='right'caption='[[3i9m]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i9m]] 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=3I9M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I9M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i9m]] 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=3I9M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I9M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AVU:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+[(2R,3R,4R)-4-FLUORO-3-HYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>AVU</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]] 1.75Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3i9j\|3i9j]], [[3i9k\|3i9k]], [[3i9l\|3i9l]], [[3i9n\|3i9n]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AVU:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+[(2R,3R,4R)-4-FLUORO-3-HYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>AVU</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD38 ([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/NAD(+)_nucleosidase NAD(+) nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.5 3.2.2.5] </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=3i9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i9m OCA], [https://pdbe.org/3i9m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i9m RCSB], [https://www.ebi.ac.uk/pdbsum/3i9m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i9m 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=3i9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i9m OCA], [https://pdbe.org/3i9m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i9m RCSB], [https://www.ebi.ac.uk/pdbsum/3i9m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i9m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CD38_HUMAN CD38_HUMAN]] Synthesizes cyclic ADP-ribose, a second messenger for glucose-induced insulin secretion. Also has cADPr hydrolase activity. Also moonlights as a receptor in cells of the immune system.	+	[https://www.uniprot.org/uniprot/CD38_HUMAN CD38_HUMAN] Synthesizes cyclic ADP-ribose, a second messenger for glucose-induced insulin secretion. Also has cADPr hydrolase activity. Also moonlights as a receptor in cells of the immune system.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Graeff, R]]	+	[[Category: Graeff R]]
-	[[Category: Hao, Q]]	+	[[Category: Hao Q]]
-	[[Category: Jiang, H]]	+	[[Category: Jiang H]]
-	[[Category: Kriksunov~~, I A~~]]	+	[[Category: Kriksunov IA]]
-	[[Category: Lee~~, H C~~]]	+	[[Category: Lee HC]]
-	[[Category: Lin, H]]	+	[[Category: Lin H]]
-	[[Category: Liu, Q]]	+	[[Category: Liu Q]]
-	[[Category: Oppenheimer, N]]	+	[[Category: Oppenheimer N]]
-	[[Category: Potter~~, B V.L~~]]	+	[[Category: Potter BVL]]
-	[[Category: Zhang, B]]	+	[[Category: Zhang B]]
-	~~[[Category: Alpha helices rich domain and alpha/beta domain]]~~	+
-	~~[[Category: Alternative splicing]]~~	+
-	~~[[Category: Covalent reaction intermediate]]~~	+
-	~~[[Category: Diabetes mellitus]]~~	+
-	~~[[Category: Disulfide bond]]~~	+
-	~~[[Category: Enzyme-analog complex]]~~	+
-	~~[[Category: Glycoprotein]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Polymorphism]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Signal-anchor]]~~	+
-	~~[[Category: Transmembrane~~]]	+

OCA at 07:46, 10 November 2021

2021-11-10T07:46:31Z

←Older revision		Revision as of 07:46, 10 November 2021
Line 1:		Line 1:

	==Crystal structure of human CD38 complexed with an analog ara-2'F-ADPR==		==Crystal structure of human CD38 complexed with an analog ara-2'F-ADPR==
-	<StructureSection load='3i9m' size='340' side='right' caption='[[3i9m]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='3i9m' size='340' side='right'caption='[[3i9m]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i9m]] 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=3I9M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3I9M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i9m]] 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=3I9M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I9M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AVU:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+[(2R,3R,4R)-4-FLUORO-3-HYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>AVU</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AVU:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+[(2R,3R,4R)-4-FLUORO-3-HYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>AVU</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i9j\|3i9j]], [[3i9k\|3i9k]], [[3i9l\|3i9l]], [[3i9n\|3i9n]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3i9j\|3i9j]], [[3i9k\|3i9k]], [[3i9l\|3i9l]], [[3i9n\|3i9n]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD38 ([~~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">CD38 ([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/NAD(+)_nucleosidase NAD(+) nucleosidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.5 3.2.2.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/NAD(+)_nucleosidase NAD(+) nucleosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.5 3.2.2.5] </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=3i9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i9m OCA], [~~http~~://pdbe.org/3i9m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3i9m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3i9m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3i9m 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=3i9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i9m OCA], [https://pdbe.org/3i9m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i9m RCSB], [https://www.ebi.ac.uk/pdbsum/3i9m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i9m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CD38_HUMAN CD38_HUMAN]] Synthesizes cyclic ADP-ribose, a second messenger for glucose-induced insulin secretion. Also has cADPr hydrolase activity. Also moonlights as a receptor in cells of the immune system.	+	[[https://www.uniprot.org/uniprot/CD38_HUMAN CD38_HUMAN]] Synthesizes cyclic ADP-ribose, a second messenger for glucose-induced insulin secretion. Also has cADPr hydrolase activity. Also moonlights as a receptor in cells of the immune system.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Graeff, R]]		[[Category: Graeff, R]]
	[[Category: Hao, Q]]		[[Category: Hao, Q]]

OCA at 09:57, 19 December 2018

2018-12-19T09:57:05Z

←Older revision		Revision as of 09:57, 19 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of human CD38 complexed with an analog ara-2'F-ADPR==		==Crystal structure of human CD38 complexed with an analog ara-2'F-ADPR==
	<StructureSection load='3i9m' size='340' side='right' caption='[[3i9m]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='3i9m' size='340' side='right' caption='[[3i9m]], [[Resolution\|resolution]] 1.75Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD38 ([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">CD38 ([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/NAD(+)_nucleosidase NAD(+) nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.5 3.2.2.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_nucleosidase NAD(+) nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.5 3.2.2.5] </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=3i9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i9m OCA], [http://pdbe.org/3i9m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i9m RCSB], [http://www.ebi.ac.uk/pdbsum/3i9m 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=3i9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i9m OCA], [http://pdbe.org/3i9m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i9m RCSB], [http://www.ebi.ac.uk/pdbsum/3i9m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3i9m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i9/3i9m_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i9/3i9m_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 49:		Line 50:
	[[Category: Zhang, B]]		[[Category: Zhang, B]]
	[[Category: Alpha helices rich domain and alpha/beta domain]]		[[Category: Alpha helices rich domain and alpha/beta domain]]
		+	[[Category: Alternative splicing]]
	[[Category: Covalent reaction intermediate]]		[[Category: Covalent reaction intermediate]]
	[[Category: Diabetes mellitus]]		[[Category: Diabetes mellitus]]
Line 57:		Line 59:
	[[Category: Membrane]]		[[Category: Membrane]]
	[[Category: Nad]]		[[Category: Nad]]
		+	[[Category: Polymorphism]]
	[[Category: Receptor]]		[[Category: Receptor]]
	[[Category: Signal-anchor]]		[[Category: Signal-anchor]]
	[[Category: Transmembrane]]		[[Category: Transmembrane]]

OCA at 15:32, 9 February 2016

2016-02-09T15:32:49Z

←Older revision		Revision as of 15:32, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3i9m' size='340' side='right' caption='[[3i9m]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='3i9m' size='340' side='right' caption='[[3i9m]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i9m]] 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=3I9M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I9M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i9m]] 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=3I9M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I9M FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AVU:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+[(2R,3R,4R)-4-FLUORO-3-HYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>AVU</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AVU:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+[(2R,3R,4R)-4-FLUORO-3-HYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>AVU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i9j\|3i9j]], [[3i9k\|3i9k]], [[3i9l\|3i9l]], [[3i9n\|3i9n]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i9j\|3i9j]], [[3i9k\|3i9k]], [[3i9l\|3i9l]], [[3i9n\|3i9n]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD38 ([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">CD38 ([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/NAD(+)_nucleosidase NAD(+) nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.5 3.2.2.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_nucleosidase NAD(+) nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.5 3.2.2.5] </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=3i9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i9m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i9m RCSB], [http://www.ebi.ac.uk/pdbsum/3i9m 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=3i9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i9m OCA], [http://pdbe.org/3i9m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i9m RCSB], [http://www.ebi.ac.uk/pdbsum/3i9m PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3i9m ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3i9m" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Graeff, R]]		[[Category: Graeff, R]]
	[[Category: Hao, Q]]		[[Category: Hao, Q]]

OCA at 07:45, 25 December 2014

2014-12-25T07:45:38Z

←Older revision		Revision as of 07:45, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3i9m]] 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=3I9M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I9M FirstGlance]. <br>		<table><tr><td colspan='2'>[[3i9m]] 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=3I9M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I9M FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AVU:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+[(2R,3R,4R)-4-FLUORO-3-HYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>AVU</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AVU:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+[(2R,3R,4R)-4-FLUORO-3-HYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>AVU</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i9j\|3i9j]], [[3i9k\|3i9k]], [[3i9l\|3i9l]], [[3i9n\|3i9n]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i9j\|3i9j]], [[3i9k\|3i9k]], [[3i9l\|3i9l]], [[3i9n\|3i9n]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD38 ([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">CD38 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_nucleosidase NAD(+) nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.5 3.2.2.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_nucleosidase NAD(+) nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.5 3.2.2.5] </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=3i9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i9m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i9m RCSB], [http://www.ebi.ac.uk/pdbsum/3i9m 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=3i9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i9m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i9m RCSB], [http://www.ebi.ac.uk/pdbsum/3i9m PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CD38_HUMAN CD38_HUMAN]] Synthesizes cyclic ADP-ribose, a second messenger for glucose-induced insulin secretion. Also has cADPr hydrolase activity. Also moonlights as a receptor in cells of the immune system.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Graeff, R.]]	+	[[Category: Graeff, R]]
-	[[Category: Hao, Q.]]	+	[[Category: Hao, Q]]
-	[[Category: Jiang, H.]]	+	[[Category: Jiang, H]]
-	[[Category: Kriksunov, I A.]]	+	[[Category: Kriksunov, I A]]
-	[[Category: Lee, H C.]]	+	[[Category: Lee, H C]]
-	[[Category: Lin, H.]]	+	[[Category: Lin, H]]
-	[[Category: Liu, Q.]]	+	[[Category: Liu, Q]]
-	[[Category: Oppenheimer, N.]]	+	[[Category: Oppenheimer, N]]
-	[[Category: Potter, B V.L.]]	+	[[Category: Potter, B V.L]]
-	[[Category: Zhang, B.]]	+	[[Category: Zhang, B]]
	[[Category: Alpha helices rich domain and alpha/beta domain]]		[[Category: Alpha helices rich domain and alpha/beta domain]]
	[[Category: Covalent reaction intermediate]]		[[Category: Covalent reaction intermediate]]

OCA at 13:23, 29 September 2014

2014-09-29T13:23:11Z

←Older revision		Revision as of 13:23, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3i9m.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of human CD38 complexed with an analog ara-2'F-ADPR==
		+	<StructureSection load='3i9m' size='340' side='right' caption='[[3i9m]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3i9m]] 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=3I9M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I9M FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AVU:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+[(2R,3R,4R)-4-FLUORO-3-HYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>AVU</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i9j\|3i9j]], [[3i9k\|3i9k]], [[3i9l\|3i9l]], [[3i9n\|3i9n]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CD38 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_nucleosidase NAD(+) nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.5 3.2.2.5] </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=3i9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i9m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i9m RCSB], [http://www.ebi.ac.uk/pdbsum/3i9m 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/i9/3i9m_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 ==
		+	Cyclic ADP-ribose (cADPR) is a universal calcium messenger molecule that regulates many physiological processes. The production and degradation of cADPR are catalyzed by a family of related enzymes, including the ADP-ribosyl cyclase from Aplysia california (ADPRAC) and CD38 from human. Although ADPRC and CD38 share a common evolutionary ancestor, their enzymatic functions toward NAD and cADPR homeostasis have evolved divergently. Thus, ADPRC can only generate cADPR from NAD (cyclase), whereas CD38, in contrast, has multiple activities, i.e. in cADPR production and degradation, as well as NAD hydrolysis (NADase). In this study, we determined a number of ADPRC and CD38 structures bound with various nucleotides. From these complexes, we elucidated the structural features required for the cyclization (cyclase) reaction of ADPRC and the NADase reaction of CD38. Using the structural approach in combination with site-directed mutagenesis, we identified Phe-174 in ADPRC as a critical residue in directing the folding of the substrate during the cyclization reaction. Thus, a point mutation of Phe-174 to glycine can turn ADPRC from a cyclase toward an NADase. The equivalent residue in CD38, Thr-221, is shown to disfavor the cyclizing folding of the substrate, resulting in NADase being the dominant activity. The comprehensive structural comparison of CD38 and APDRC presented in this study thus provides insights into the structural determinants for the functional evolution from a cyclase to a hydrolase.

-	~~{{STRUCTURE_3i9m\| PDB=3i9m \| SCENE= }}~~	+	Structural basis for enzymatic evolution from a dedicated ADP-ribosyl cyclase to a multifunctional NAD hydrolase.,Liu Q, Graeff R, Kriksunov IA, Jiang H, Zhang B, Oppenheimer N, Lin H, Potter BV, Lee HC, Hao Q J Biol Chem. 2009 Oct 2;284(40):27637-45. Epub 2009 Jul 28. PMID:19640846<ref>PMID:19640846</ref>

-	~~===Crystal structure~~ of ~~human CD38 complexed with an analog ara-2'F-ADPR===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19640846}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3i9m]] 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=3I9M OCA].~~	+

	==See Also==		==See Also==
-	*[[Cluster of Differentiation 38\|Cluster of Differentiation 38]]	+	*[[Cluster of Differentiation CD38\|Cluster of Differentiation CD38]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019640846<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Graeff, R.]]		[[Category: Graeff, R.]]

OCA at 14:19, 20 October 2012

2012-10-20T14:19:06Z

←Older revision		Revision as of 14:19, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3i9m]] is a 2 chain structure ~~of [[Cluster of Differentiation 38]]~~ 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=3I9M OCA].	+	[[3i9m]] 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=3I9M OCA].

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

OCA at 14:45, 26 July 2012

2012-07-26T14:45:53Z

←Older revision		Revision as of 14:45, 26 July 2012
Line 1:		Line 1:
	[[Image:3i9m.png\|left\|200px]]		[[Image:3i9m.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3i9m", 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.
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	{{STRUCTURE_3i9m\| PDB=3i9m \| SCENE= }}		{{STRUCTURE_3i9m\| PDB=3i9m \| SCENE= }}

	===Crystal structure of human CD38 complexed with an analog ara-2'F-ADPR===		===Crystal structure of human CD38 complexed with an analog ara-2'F-ADPR===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19640846}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19640846 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19640846}}		{{ABSTRACT_PUBMED_19640846}}

OCA at 15:27, 5 June 2012

2012-06-05T15:27:05Z

←Older revision		Revision as of 15:27, 5 June 2012
Line 19:		Line 19:

	==About this Structure==		==About this Structure==
-	[[3i9m]] is a 2 chain structure of ~~[[ADP-ribosyl cyclase 1]] and~~ [[Cluster of Differentiation 38]] 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=3I9M OCA].	+	[[3i9m]] is a 2 chain structure of [[Cluster of Differentiation 38]] 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=3I9M OCA].

	==See Also==		==See Also==
-	*[[~~ADP-ribosyl cyclase 1]]~~	+	*[[Cluster of Differentiation 38\|Cluster of Differentiation 38]]
-	*[[Cluster of Differentiation 38]]	+

	==Reference==		==Reference==
Line 39:		Line 38:
	[[Category: Zhang, B.]]		[[Category: Zhang, B.]]
	[[Category: Alpha helices rich domain and alpha/beta domain]]		[[Category: Alpha helices rich domain and alpha/beta domain]]
-	[[Category: Alternative splicing]]
	[[Category: Covalent reaction intermediate]]		[[Category: Covalent reaction intermediate]]
	[[Category: Diabetes mellitus]]		[[Category: Diabetes mellitus]]
Line 48:		Line 46:
	[[Category: Membrane]]		[[Category: Membrane]]
	[[Category: Nad]]		[[Category: Nad]]
-	[[Category: Polymorphism]]
	[[Category: Receptor]]		[[Category: Receptor]]
	[[Category: Signal-anchor]]		[[Category: Signal-anchor]]
	[[Category: Transmembrane]]		[[Category: Transmembrane]]

OCA at 11:47, 26 May 2011

2011-05-26T11:47:55Z

←Older revision		Revision as of 11:47, 26 May 2011
Line 26:		Line 26:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19640846~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019640846</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Graeff, R.]]		[[Category: Graeff, R.]]