2jdz - Revision history

OCA at 14:44, 13 December 2023

OCA — Wed, 13 Dec 2023 14:44:34 GMT

←Older revision		Revision as of 14:44, 13 December 2023
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	<StructureSection load='2jdz' size='340' side='right'caption='[[2jdz]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2jdz' size='340' side='right'caption='[[2jdz]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2jdz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Diogu Diogu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JDZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2jdz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dioclea_guianensis Dioclea guianensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JDZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</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]] 2.1Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1h9p\|1h9p]], [[1h9w\|1h9w]], [[2je7\|2je7]], [[2je9\|2je9]], [[2jec\|2jec]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</scene></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=2jdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jdz OCA], [https://pdbe.org/2jdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jdz RCSB], [https://www.ebi.ac.uk/pdbsum/2jdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jdz 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=2jdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jdz OCA], [https://pdbe.org/2jdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jdz RCSB], [https://www.ebi.ac.uk/pdbsum/2jdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jdz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/LECA_DIOGU LECA_DIOGU]] D-mannose/D-glucose-binding lectin. Has anti-inflammatory activity in rats. Induces histamine release in mast cells from rat. Induces lymphocyte proliferation and IFNG production.<ref>PMID:1398779</ref> <ref>PMID:7524287</ref> <ref>PMID:18472821</ref> <ref>PMID:9575151</ref> <ref>PMID:10747944</ref>	+	[https://www.uniprot.org/uniprot/LECA_DIOGU LECA_DIOGU] D-mannose/D-glucose-binding lectin. Has anti-inflammatory activity in rats. Induces histamine release in mast cells from rat. Induces lymphocyte proliferation and IFNG production.<ref>PMID:1398779</ref> <ref>PMID:7524287</ref> <ref>PMID:18472821</ref> <ref>PMID:9575151</ref> <ref>PMID:10747944</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Diogu~~]]	+	[[Category: Dioclea guianensis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Calvete~~, J J~~]]	+	[[Category: Calvete JJ]]
-	[[Category: Cavada~~, B S~~]]	+	[[Category: Cavada BS]]
-	[[Category: Nagano~~, C S~~]]	+	[[Category: Nagano CS]]
-	[[Category: Sanz, L]]	+	[[Category: Sanz L]]
-	~~[[Category: Carbohydrate-binding protein]]~~	+
-	~~[[Category: Legume lectin]]~~	+
-	~~[[Category: Metal-binding~~]]	+

OCA at 11:26, 31 March 2021

OCA — Wed, 31 Mar 2021 11:26:14 GMT

←Older revision		Revision as of 11:26, 31 March 2021
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	<StructureSection load='2jdz' size='340' side='right'caption='[[2jdz]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2jdz' size='340' side='right'caption='[[2jdz]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2jdz]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Diogu Diogu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2JDZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2jdz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Diogu Diogu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JDZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h9p\|1h9p]], [[1h9w\|1h9w]], [[2je7\|2je7]], [[2je9\|2je9]], [[2jec\|2jec]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1h9p\|1h9p]], [[1h9w\|1h9w]], [[2je7\|2je7]], [[2je9\|2je9]], [[2jec\|2jec]]</div></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=2jdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jdz OCA], [~~http~~://pdbe.org/2jdz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2jdz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2jdz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2jdz 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=2jdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jdz OCA], [https://pdbe.org/2jdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jdz RCSB], [https://www.ebi.ac.uk/pdbsum/2jdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jdz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/LECA_DIOGU LECA_DIOGU]] D-mannose/D-glucose-binding lectin. Has anti-inflammatory activity in rats. Induces histamine release in mast cells from rat. Induces lymphocyte proliferation and IFNG production.<ref>PMID:1398779</ref> <ref>PMID:7524287</ref> <ref>PMID:18472821</ref> <ref>PMID:9575151</ref> <ref>PMID:10747944</ref>	+	[[https://www.uniprot.org/uniprot/LECA_DIOGU LECA_DIOGU]] D-mannose/D-glucose-binding lectin. Has anti-inflammatory activity in rats. Induces histamine release in mast cells from rat. Induces lymphocyte proliferation and IFNG production.<ref>PMID:1398779</ref> <ref>PMID:7524287</ref> <ref>PMID:18472821</ref> <ref>PMID:9575151</ref> <ref>PMID:10747944</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 12:06, 10 May 2019

OCA — Fri, 10 May 2019 12:06:02 GMT

←Older revision		Revision as of 12:06, 10 May 2019
Line 1:		Line 1:

	==Crystal structure of recombinant Dioclea guianensis lectin complexed with 5-bromo-4-chloro-3-indolyl-a-D-mannose==		==Crystal structure of recombinant Dioclea guianensis lectin complexed with 5-bromo-4-chloro-3-indolyl-a-D-mannose==
-	<StructureSection load='2jdz' size='340' side='right' caption='[[2jdz]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='2jdz' size='340' side='right'caption='[[2jdz]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jdz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Diogu Diogu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JDZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jdz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Diogu Diogu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JDZ FirstGlance]. <br>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Diogu]]		[[Category: Diogu]]
		+	[[Category: Large Structures]]
	[[Category: Calvete, J J]]		[[Category: Calvete, J J]]
	[[Category: Cavada, B S]]		[[Category: Cavada, B S]]

OCA at 07:06, 11 July 2018

OCA — Wed, 11 Jul 2018 07:06:29 GMT

←Older revision		Revision as of 07:06, 11 July 2018
Line 1:		Line 1:
		+
	==Crystal structure of recombinant Dioclea guianensis lectin complexed with 5-bromo-4-chloro-3-indolyl-a-D-mannose==		==Crystal structure of recombinant Dioclea guianensis lectin complexed with 5-bromo-4-chloro-3-indolyl-a-D-mannose==
	<StructureSection load='2jdz' size='340' side='right' caption='[[2jdz]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2jdz' size='340' side='right' caption='[[2jdz]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h9p\|1h9p]], [[1h9w\|1h9w]], [[2je7\|2je7]], [[2je9\|2je9]], [[2jec\|2jec]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h9p\|1h9p]], [[1h9w\|1h9w]], [[2je7\|2je7]], [[2je9\|2je9]], [[2jec\|2jec]]</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=2jdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jdz OCA], [http://pdbe.org/2jdz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jdz RCSB], [http://www.ebi.ac.uk/pdbsum/2jdz 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=2jdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jdz OCA], [http://pdbe.org/2jdz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jdz RCSB], [http://www.ebi.ac.uk/pdbsum/2jdz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jdz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jd/2jdz_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jd/2jdz_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 08:21, 9 February 2016

OCA — Tue, 09 Feb 2016 08:21:36 GMT

←Older revision		Revision as of 08:21, 9 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2jdz ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:24, 10 September 2015

OCA — Thu, 10 Sep 2015 20:24:15 GMT

←Older revision		Revision as of 20:24, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2jdz' size='340' side='right' caption='[[2jdz]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2jdz' size='340' side='right' caption='[[2jdz]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2jdz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Dioclea_guianensis Dioclea guianensis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JDZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2jdz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Diogu Diogu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JDZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h9p\|1h9p]], [[1h9w\|1h9w]], [[2je7\|2je7]], [[2je9\|2je9]], [[2jec\|2jec]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h9p\|1h9p]], [[1h9w\|1h9w]], [[2je7\|2je7]], [[2je9\|2je9]], [[2jec\|2jec]]</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=2jdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jdz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jdz RCSB], [http://www.ebi.ac.uk/pdbsum/2jdz 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=2jdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jdz OCA], [http://pdbe.org/2jdz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jdz RCSB], [http://www.ebi.ac.uk/pdbsum/2jdz PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2jdz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dioclea guianensis~~]]	+	[[Category: Diogu]]
	[[Category: Calvete, J J]]		[[Category: Calvete, J J]]
	[[Category: Cavada, B S]]		[[Category: Cavada, B S]]

OCA at 05:40, 25 December 2014

OCA — Thu, 25 Dec 2014 05:40:43 GMT

←Older revision		Revision as of 05:40, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jdz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dioclea_guianensis Dioclea guianensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JDZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jdz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dioclea_guianensis Dioclea guianensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JDZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h9p\|1h9p]], [[1h9w\|1h9w]], [[2je7\|2je7]], [[2je9\|2je9]], [[2jec\|2jec]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h9p\|1h9p]], [[1h9w\|1h9w]], [[2je7\|2je7]], [[2je9\|2je9]], [[2jec\|2jec]]</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=2jdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jdz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jdz RCSB], [http://www.ebi.ac.uk/pdbsum/2jdz 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=2jdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jdz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jdz RCSB], [http://www.ebi.ac.uk/pdbsum/2jdz PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LECA_DIOGU LECA_DIOGU]] D-mannose/D-glucose-binding lectin. Has anti-inflammatory activity in rats. Induces histamine release in mast cells from rat. Induces lymphocyte proliferation and IFNG production.<ref>PMID:1398779</ref> <ref>PMID:7524287</ref> <ref>PMID:18472821</ref> <ref>PMID:9575151</ref> <ref>PMID:10747944</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Dioclea guianensis]]		[[Category: Dioclea guianensis]]
-	[[Category: Calvete, J J.]]	+	[[Category: Calvete, J J]]
-	[[Category: Cavada, B S.]]	+	[[Category: Cavada, B S]]
-	[[Category: Nagano, C S.]]	+	[[Category: Nagano, C S]]
-	[[Category: Sanz, L.]]	+	[[Category: Sanz, L]]
	[[Category: Carbohydrate-binding protein]]		[[Category: Carbohydrate-binding protein]]
	[[Category: Legume lectin]]		[[Category: Legume lectin]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]

OCA at 07:06, 9 June 2014

OCA — Mon, 09 Jun 2014 07:06:56 GMT

←Older revision		Revision as of 07:06, 9 June 2014
Line 1:		Line 1:
-	[[~~Image:~~2jdz.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of recombinant Dioclea guianensis lectin complexed with 5-bromo-4-chloro-3-indolyl-a-D-mannose==
		+	<StructureSection load='2jdz' size='340' side='right' caption='[[2jdz]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2jdz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dioclea_guianensis Dioclea guianensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JDZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h9p\|1h9p]], [[1h9w\|1h9w]], [[2je7\|2je7]], [[2je9\|2je9]], [[2jec\|2jec]]</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=2jdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jdz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jdz RCSB], [http://www.ebi.ac.uk/pdbsum/2jdz 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/jd/2jdz_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 structural ground underlying the pH-dependency of the dimer-tetramer transition of Diocleinae lectins was investigated by equilibrium sedimentation and X-ray crystal structure determination of wild-type and site-directed mutants of recombinant lectins. Synthetic genes coding for the full-length alpha-chains of the seed lectins of Dioclea guianensis (termed r-alphaDguia) and Dioclea grandiflora (termed r-alphaDGL) were designed and expressed in Escherichia coli. This pioneering approach, which will be described in detail in the present paper, yielded recombinant lectins displaying carbohydrate-binding activity, dimer-tetramer equilibria and crystal structures indistinguishable from their natural homologues. Conversion of the pH-stable tetrameric r-alphaDGL into a structure exhibiting pH-dependent dimer-tetramer transition was accomplished through mutations that abolished the interdimeric interactions at the central cavity of the tetrameric lectins. Both the central and the peripheral interacting regions bear structural information for formation of the canonical legume lectin tetramer. We hypothesize that the strength of the ionic contacts at these sites may be modulated by the pH, leading to dissociation of those lectin structures that are not locked into a pH-stable tetramer through interdimeric contacts networking the central cavity loops.

-	~~{{STRUCTURE_2jdz\| PDB=2jdz \| SCENE= }}~~	+	Insights into the structural basis of the pH-dependent dimer-tetramer equilibrium through crystallographic analysis of recombinant Diocleinae lectins.,Nagano CS, Calvete JJ, Barettino D, Perez A, Cavada BS, Sanz L Biochem J. 2008 Jan 15;409(2):417-28. PMID:17937659<ref>PMID:17937659</ref>

-	~~===Crystal structure~~ of ~~recombinant Dioclea guianensis lectin complexed with 5-bromo-4-chloro-3-indolyl-a-D-mannose===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17937659}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2jdz]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Dioclea_guianensis Dioclea guianensis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2JDZ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017937659<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Dioclea guianensis]]		[[Category: Dioclea guianensis]]
	[[Category: Calvete, J J.]]		[[Category: Calvete, J J.]]

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

OCA — Wed, 29 Aug 2012 05:14:28 GMT

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

←Older revision

Revision as of 05:14, 29 August 2012

OCA at 05:14, 29 August 2012

OCA — Wed, 29 Aug 2012 05:14:23 GMT

←Older revision		Revision as of 05:14, 29 August 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2jdz.png\|left\|200px]]		[[Image:2jdz.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2jdz", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2jdz\| PDB=2jdz \| SCENE= }}		{{STRUCTURE_2jdz\| PDB=2jdz \| SCENE= }}

-	===~~CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GUIANENSIS LECTIN COMPLEXED WITH~~ 5-~~BROMO~~-4-~~CHLORO~~-3-~~INDOLYL~~-A-D-~~MANNOSE~~===	+	===Crystal structure of recombinant Dioclea guianensis lectin complexed with 5-bromo-4-chloro-3-indolyl-a-D-mannose===

		+	{{ABSTRACT_PUBMED_17937659}}

	==About this Structure==		==About this Structure==
-	~~2JDZ~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Dioclea_guianensis Dioclea guianensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDZ OCA].	+	[[2jdz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dioclea_guianensis Dioclea guianensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JDZ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:017937659</ref><references group="xtra"/>
	[[Category: Dioclea guianensis]]		[[Category: Dioclea guianensis]]
	[[Category: Calvete, J J.]]		[[Category: Calvete, J J.]]
Line 20:		Line 17:
	[[Category: Nagano, C S.]]		[[Category: Nagano, C S.]]
	[[Category: Sanz, L.]]		[[Category: Sanz, L.]]
-	[[Category: Calcium]]
	[[Category: Carbohydrate-binding protein]]		[[Category: Carbohydrate-binding protein]]
-	[[Category: Cona-like]]
-	[[Category: Lectin]]
	[[Category: Legume lectin]]		[[Category: Legume lectin]]
-	[[Category: Manganese]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
-	[[Category: Recombinant lectin]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 08:19:08 2009''