2r8q - Revision history

OCA at 09:20, 21 February 2024

OCA — Wed, 21 Feb 2024 09:20:51 GMT

←Older revision		Revision as of 09:20, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2r8q' size='340' side='right'caption='[[2r8q]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='2r8q' size='340' side='right'caption='[[2r8q]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r8q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Leima Leima~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R8Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r8q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R8Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=IBM:3-ISOBUTYL~~-1~~-METHYLXANTHINE'>IBM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~PDEB1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=5664 LEIMA])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IBM:3-ISOBUTYL-1-METHYLXANTHINE'>IBM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] </~~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=2r8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8q OCA], [https://pdbe.org/2r8q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r8q RCSB], [https://www.ebi.ac.uk/pdbsum/2r8q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8q 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=2r8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8q OCA], [https://pdbe.org/2r8q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r8q RCSB], [https://www.ebi.ac.uk/pdbsum/2r8q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8q ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q6S996_LEIMA Q6S996_LEIMA]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</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=2r8q 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=2r8q ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Human leishmaniasis is a major public health problem in many countries, but chemotherapy is in an unsatisfactory state. Leishmania major phosphodiesterases (LmjPDEs) have been shown to play important roles in cell proliferation and apoptosis of the parasite. Thus LmjPDE inhibitors may potentially represent a novel class of drugs for the treatment of leishmaniasis. Reported here are the kinetic characterization of the LmjPDEB1 catalytic domain and its crystal structure as a complex with 3-isobutyl-1-methylxanthine (IBMX) at 1.55 A resolution. The structure of LmjPDEB1 is similar to that of human PDEs. IBMX stacks against the conserved phenylalanine and forms a hydrogen bond with the invariant glutamine, in a pattern common to most inhibitors bound to human PDEs. However, an extensive structural comparison reveals subtle, but significant differences between the active sites of LmjPDEB1 and human PDEs. In addition, a pocket next to the inhibitor binding site is found to be unique to LmjPDEB1. This pocket is isolated by two gating residues in human PDE families, but constitutes a natural expansion of the inhibitor binding pocket in LmjPDEB1. The structure particularity might be useful for the development of parasite-selective inhibitors for the treatment of leishmaniasis.
-
-	Crystal structure of the Leishmania major phosphodiesterase LmjPDEB1 and insight into the design of the parasite-selective inhibitors.,Wang H, Yan Z, Geng J, Kunz S, Seebeck T, Ke H Mol Microbiol. 2007 Nov;66(4):1029-38. Epub 2007 Oct 17. PMID:17944832<ref>PMID:17944832</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2r8q" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]		*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Leima~~]]	+	[[Category: Leishmania major]]
-	[[Category: Geng, J]]	+	[[Category: Geng J]]
-	[[Category: Ke, H]]	+	[[Category: Ke H]]
-	[[Category: Kunz, S]]	+	[[Category: Kunz S]]
-	[[Category: Seebeck, T]]	+	[[Category: Seebeck T]]
-	[[Category: Wang, H]]	+	[[Category: Wang H]]
-	[[Category: Yan, Z]]	+	[[Category: Yan Z]]
-	~~[[Category: Camp phosphodiesterase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Leishimaniasis]]~~	+
-	~~[[Category: Parasite inhibitor selectivity~~]]	+

OCA at 04:18, 2 July 2021

OCA — Fri, 02 Jul 2021 04:18:11 GMT

←Older revision		Revision as of 04:18, 2 July 2021
Line 1:		Line 1:

	==Structure of LmjPDEB1 in complex with IBMX==		==Structure of LmjPDEB1 in complex with IBMX==
-	<StructureSection load='2r8q' size='340' side='right' caption='[[2r8q]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='2r8q' size='340' side='right'caption='[[2r8q]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r8q]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Leima Leima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2R8Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r8q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Leima Leima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R8Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IBM:3-ISOBUTYL-1-METHYLXANTHINE'>IBM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IBM:3-ISOBUTYL-1-METHYLXANTHINE'>IBM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDEB1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5664 LEIMA])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDEB1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5664 LEIMA])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] </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=2r8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8q OCA], [~~http~~://pdbe.org/2r8q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2r8q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2r8q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8q 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=2r8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8q OCA], [https://pdbe.org/2r8q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r8q RCSB], [https://www.ebi.ac.uk/pdbsum/2r8q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8q ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Phosphodiesterase\|Phosphodiesterase]]	+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]		[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
		+	[[Category: Large Structures]]
	[[Category: Leima]]		[[Category: Leima]]
	[[Category: Geng, J]]		[[Category: Geng, J]]

OCA at 10:45, 5 September 2018

OCA — Wed, 05 Sep 2018 10:45:59 GMT

←Older revision		Revision as of 10:45, 5 September 2018
Line 1:		Line 1:
		+
	==Structure of LmjPDEB1 in complex with IBMX==		==Structure of LmjPDEB1 in complex with IBMX==
	<StructureSection load='2r8q' size='340' side='right' caption='[[2r8q]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='2r8q' size='340' side='right' caption='[[2r8q]], [[Resolution\|resolution]] 1.50Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDEB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5664 LEIMA])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDEB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5664 LEIMA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] </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=2r8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8q OCA], [http://pdbe.org/2r8q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r8q RCSB], [http://www.ebi.ac.uk/pdbsum/2r8q 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=2r8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8q OCA], [http://pdbe.org/2r8q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r8q RCSB], [http://www.ebi.ac.uk/pdbsum/2r8q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2r8q 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/r8/2r8q_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r8/2r8q_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 19:52, 9 February 2016

OCA — Tue, 09 Feb 2016 19:52:10 GMT

←Older revision		Revision as of 19:52, 9 February 2016
Line 16:		Line 16:
	<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=2r8q ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:30, 11 September 2015

OCA — Fri, 11 Sep 2015 01:30:17 GMT

←Older revision		Revision as of 01:30, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2r8q' size='340' side='right' caption='[[2r8q]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='2r8q' size='340' side='right' caption='[[2r8q]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r8q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Leishmania_major Leishmania major~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r8q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leima Leima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IBM:3-ISOBUTYL-1-METHYLXANTHINE'>IBM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IBM:3-ISOBUTYL-1-METHYLXANTHINE'>IBM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDEB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5664 ~~Leishmania major~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDEB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5664 LEIMA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] </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=2r8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r8q RCSB], [http://www.ebi.ac.uk/pdbsum/2r8q 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=2r8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8q OCA], [http://pdbe.org/2r8q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r8q RCSB], [http://www.ebi.ac.uk/pdbsum/2r8q 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 2r8q" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]		[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
-	[[Category: ~~Leishmania major~~]]	+	[[Category: Leima]]
	[[Category: Geng, J]]		[[Category: Geng, J]]
	[[Category: Ke, H]]		[[Category: Ke, H]]

OCA at 13:12, 19 January 2015

OCA — Mon, 19 Jan 2015 13:12:17 GMT

←Older revision		Revision as of 13:12, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2r8q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[2r8q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8Q FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IBM:3-ISOBUTYL-1-METHYLXANTHINE'>IBM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IBM:3-ISOBUTYL-1-METHYLXANTHINE'>IBM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDEB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5664 Leishmania major])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDEB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5664 Leishmania major])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] </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=2r8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r8q RCSB], [http://www.ebi.ac.uk/pdbsum/2r8q 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=2r8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r8q RCSB], [http://www.ebi.ac.uk/pdbsum/2r8q 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 35:		Line 35:
	[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]		[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
	[[Category: Leishmania major]]		[[Category: Leishmania major]]
-	[[Category: Geng, J.]]	+	[[Category: Geng, J]]
-	[[Category: Ke, H.]]	+	[[Category: Ke, H]]
-	[[Category: Kunz, S.]]	+	[[Category: Kunz, S]]
-	[[Category: Seebeck, T.]]	+	[[Category: Seebeck, T]]
-	[[Category: Wang, H.]]	+	[[Category: Wang, H]]
-	[[Category: Yan, Z.]]	+	[[Category: Yan, Z]]
	[[Category: Camp phosphodiesterase]]		[[Category: Camp phosphodiesterase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Leishimaniasis]]		[[Category: Leishimaniasis]]
	[[Category: Parasite inhibitor selectivity]]		[[Category: Parasite inhibitor selectivity]]

OCA at 06:15, 29 September 2014

OCA — Mon, 29 Sep 2014 06:15:31 GMT

←Older revision		Revision as of 06:15, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2r8q.~~png~~\|~~left~~\|200px]]	+	==Structure of LmjPDEB1 in complex with IBMX==
		+	<StructureSection load='2r8q' size='340' side='right' caption='[[2r8q]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2r8q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R8Q FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IBM:3-ISOBUTYL-1-METHYLXANTHINE'>IBM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDEB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5664 Leishmania major])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] </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=2r8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r8q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r8q RCSB], [http://www.ebi.ac.uk/pdbsum/2r8q 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/r8/2r8q_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 ==
		+	Human leishmaniasis is a major public health problem in many countries, but chemotherapy is in an unsatisfactory state. Leishmania major phosphodiesterases (LmjPDEs) have been shown to play important roles in cell proliferation and apoptosis of the parasite. Thus LmjPDE inhibitors may potentially represent a novel class of drugs for the treatment of leishmaniasis. Reported here are the kinetic characterization of the LmjPDEB1 catalytic domain and its crystal structure as a complex with 3-isobutyl-1-methylxanthine (IBMX) at 1.55 A resolution. The structure of LmjPDEB1 is similar to that of human PDEs. IBMX stacks against the conserved phenylalanine and forms a hydrogen bond with the invariant glutamine, in a pattern common to most inhibitors bound to human PDEs. However, an extensive structural comparison reveals subtle, but significant differences between the active sites of LmjPDEB1 and human PDEs. In addition, a pocket next to the inhibitor binding site is found to be unique to LmjPDEB1. This pocket is isolated by two gating residues in human PDE families, but constitutes a natural expansion of the inhibitor binding pocket in LmjPDEB1. The structure particularity might be useful for the development of parasite-selective inhibitors for the treatment of leishmaniasis.

-	~~{{STRUCTURE_2r8q\| PDB=2r8q \| SCENE= }}~~	+	Crystal structure of the Leishmania major phosphodiesterase LmjPDEB1 and insight into the design of the parasite-selective inhibitors.,Wang H, Yan Z, Geng J, Kunz S, Seebeck T, Ke H Mol Microbiol. 2007 Nov;66(4):1029-38. Epub 2007 Oct 17. PMID:17944832<ref>PMID:17944832</ref>

-	~~===Structure~~ of ~~LmjPDEB1 in complex with IBMX===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17944832}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2r8q]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Leishmania_major Leishmania major]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2R8Q OCA].~~	+

	==See Also==		==See Also==
	*[[Phosphodiesterase\|Phosphodiesterase]]		*[[Phosphodiesterase\|Phosphodiesterase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017944832<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]		[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
	[[Category: Leishmania major]]		[[Category: Leishmania major]]

OCA at 14:56, 20 October 2012

OCA — Sat, 20 Oct 2012 14:56:48 GMT

←Older revision		Revision as of 14:56, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2r8q]] is a 2 chain structure ~~of [[Phosphodiesterase]]~~ with sequence from [http://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8Q OCA].	+	[[2r8q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R8Q OCA].

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

OCA at 16:46, 26 July 2012

OCA — Thu, 26 Jul 2012 16:46:25 GMT

←Older revision		Revision as of 16:46, 26 July 2012
Line 1:		Line 1:
	[[Image:2r8q.png\|left\|200px]]		[[Image:2r8q.png\|left\|200px]]

-	<!--
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-	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_2r8q\| PDB=2r8q \| SCENE= }}		{{STRUCTURE_2r8q\| PDB=2r8q \| SCENE= }}

	===Structure of LmjPDEB1 in complex with IBMX===		===Structure of LmjPDEB1 in complex with IBMX===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17944832}}, adds the Publication Abstract to the page
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	{{ABSTRACT_PUBMED_17944832}}		{{ABSTRACT_PUBMED_17944832}}

OCA: Protected "2r8q" [edit=sysop:move=sysop]

OCA — Sat, 02 Jun 2012 08:52:43 GMT

Protected "2r8q" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:52, 2 June 2012