3l6b - Revision history

OCA at 06:40, 3 April 2024

OCA — Wed, 03 Apr 2024 06:40:35 GMT

←Older revision		Revision as of 06:40, 3 April 2024
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	<StructureSection load='3l6b' size='340' side='right'caption='[[3l6b]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='3l6b' size='340' side='right'caption='[[3l6b]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3l6b]] is a 1 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=3L6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L6B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3l6b]] is a 1 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=3L6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L6B FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>~~, ~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-~~5~~-PHOSPHATE'>PLP</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='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3l6c\|3l6c]], [[3l6r\|3l6r]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">SRR~~ (~~[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/Serine_racemase Serine racemase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.18 5.1.1.18]~~ </~~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=3l6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l6b OCA], [https://pdbe.org/3l6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l6b RCSB], [https://www.ebi.ac.uk/pdbsum/3l6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l6b 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=3l6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l6b OCA], [https://pdbe.org/3l6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l6b RCSB], [https://www.ebi.ac.uk/pdbsum/3l6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l6b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SRR_HUMAN SRR_HUMAN]] Catalyzes the synthesis of D-serine from L-serine. D-serine is a key coagonist with glutamate at NMDA receptors. Has dehydratase activity towards both L-serine and D-serine.<ref>PMID:11054547</ref> <ref>PMID:20106978</ref>	+	[https://www.uniprot.org/uniprot/SRR_HUMAN SRR_HUMAN] Catalyzes the synthesis of D-serine from L-serine. D-serine is a key coagonist with glutamate at NMDA receptors. Has dehydratase activity towards both L-serine and D-serine.<ref>PMID:11054547</ref> <ref>PMID:20106978</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3l6b 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=3l6b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Serine racemase is responsible for the synthesis of D-serine, an endogenous co-agonist for N-methyl-D-aspartate receptor-type glutamate receptors (NMDARs). This pyridoxal 5'-phosphate-dependent enzyme is involved both in the reversible conversion of L- to D-serine and serine catabolism by alpha,beta-elimination of water, thereby regulating D-serine levels. Because D-serine affects NMDAR signaling throughout the brain, serine racemase is a promising target for the treatment of disorders related to NMDAR dysfunction. To provide a molecular basis for rational drug design the x-ray crystal structures of human and rat serine racemase were determined at 1.5- and 2.1-A resolution, respectively, and in the presence and absence of the orthosteric inhibitor malonate. The structures revealed a fold typical of beta-family pyridoxal 5'-phosphate enzymes, with both a large domain and a flexible small domain associated into a symmetric dimer, and indicated a ligand-induced rearrangement of the small domain that organizes the active site for specific turnover of the substrate.
-
-	The structure of mammalian serine racemase: evidence for conformational changes upon inhibitor binding.,Smith MA, Mack V, Ebneth A, Moraes I, Felicetti B, Wood M, Schonfeld D, Mather O, Cesura A, Barker J J Biol Chem. 2010 Apr 23;285(17):12873-81. Epub 2010 Jan 27. PMID:20106978<ref>PMID:20106978</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3l6b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Serine racemase]]~~	+	[[Category: Barker J]]
-	[[Category: Barker, J]]	+	[[Category: Cesura A]]
-	[[Category: Cesura, A]]	+	[[Category: Ebneth A]]
-	[[Category: Ebneth, A]]	+	[[Category: Felicetti B]]
-	[[Category: Felicetti, B]]	+	[[Category: Mack V]]
-	[[Category: Mack, V]]	+	[[Category: Moraes I]]
-	[[Category: Moraes, I]]	+	[[Category: Smith MA]]
-	[[Category: Smith~~, M A]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Plp]]~~	+
-	~~[[Category: Pyridoxal phosphate~~]]	+

OCA at 07:53, 10 November 2021

OCA — Wed, 10 Nov 2021 07:53:03 GMT

←Older revision		Revision as of 07:53, 10 November 2021
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	==X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor==		==X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor==
-	<StructureSection load='3l6b' size='340' side='right' caption='[[3l6b]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='3l6b' size='340' side='right'caption='[[3l6b]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3l6b]] is a 1 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=3L6B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3L6B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3l6b]] is a 1 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=3L6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L6B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3l6c\|3l6c]], [[3l6r\|3l6r]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3l6c\|3l6c]], [[3l6r\|3l6r]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SRR ([~~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">SRR ([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/Serine_racemase Serine racemase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.18 5.1.1.18] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Serine_racemase Serine racemase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.18 5.1.1.18] </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=3l6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l6b OCA], [~~http~~://pdbe.org/3l6b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3l6b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3l6b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3l6b 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=3l6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l6b OCA], [https://pdbe.org/3l6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l6b RCSB], [https://www.ebi.ac.uk/pdbsum/3l6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l6b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SRR_HUMAN SRR_HUMAN]] Catalyzes the synthesis of D-serine from L-serine. D-serine is a key coagonist with glutamate at NMDA receptors. Has dehydratase activity towards both L-serine and D-serine.<ref>PMID:11054547</ref> <ref>PMID:20106978</ref>	+	[[https://www.uniprot.org/uniprot/SRR_HUMAN SRR_HUMAN]] Catalyzes the synthesis of D-serine from L-serine. D-serine is a key coagonist with glutamate at NMDA receptors. Has dehydratase activity towards both L-serine and D-serine.<ref>PMID:11054547</ref> <ref>PMID:20106978</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Serine racemase]]		[[Category: Serine racemase]]
	[[Category: Barker, J]]		[[Category: Barker, J]]

OCA at 07:10, 2 January 2019

OCA — Wed, 02 Jan 2019 07:10:30 GMT

←Older revision		Revision as of 07:10, 2 January 2019
Line 1:		Line 1:
		+
	==X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor==		==X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor==
	<StructureSection load='3l6b' size='340' side='right' caption='[[3l6b]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='3l6b' size='340' side='right' caption='[[3l6b]], [[Resolution\|resolution]] 1.50Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SRR ([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">SRR ([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/Serine_racemase Serine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.18 5.1.1.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine_racemase Serine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.18 5.1.1.18] </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=3l6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l6b OCA], [http://pdbe.org/3l6b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3l6b RCSB], [http://www.ebi.ac.uk/pdbsum/3l6b 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=3l6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l6b OCA], [http://pdbe.org/3l6b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3l6b RCSB], [http://www.ebi.ac.uk/pdbsum/3l6b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3l6b 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/l6/3l6b_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l6/3l6b_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 13:41, 7 February 2016

OCA — Sun, 07 Feb 2016 13:41:20 GMT

←Older revision		Revision as of 13:41, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3l6b' size='340' side='right' caption='[[3l6b]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='3l6b' size='340' side='right' caption='[[3l6b]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3l6b]] is a 1 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=3L6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L6B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3l6b]] is a 1 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=3L6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L6B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3l6c\|3l6c]], [[3l6r\|3l6r]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3l6c\|3l6c]], [[3l6r\|3l6r]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SRR ([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">SRR ([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/Serine_racemase Serine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.18 5.1.1.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine_racemase Serine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.18 5.1.1.18] </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=3l6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l6b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3l6b RCSB], [http://www.ebi.ac.uk/pdbsum/3l6b 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=3l6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l6b OCA], [http://pdbe.org/3l6b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3l6b RCSB], [http://www.ebi.ac.uk/pdbsum/3l6b 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=3l6b 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 3l6b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Serine racemase]]		[[Category: Serine racemase]]
	[[Category: Barker, J]]		[[Category: Barker, J]]

OCA at 15:29, 24 December 2014

OCA — Wed, 24 Dec 2014 15:29:33 GMT

←Older revision		Revision as of 15:29, 24 December 2014
Line 9:		Line 9:
	<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=3l6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l6b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3l6b RCSB], [http://www.ebi.ac.uk/pdbsum/3l6b 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=3l6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l6b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3l6b RCSB], [http://www.ebi.ac.uk/pdbsum/3l6b PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SRR_HUMAN SRR_HUMAN]] Catalyzes the synthesis of D-serine from L-serine. D-serine is a key coagonist with glutamate at NMDA receptors. Has dehydratase activity towards both L-serine and D-serine.<ref>PMID:11054547</ref> <ref>PMID:20106978</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 16:21, 18 December 2014

OCA — Thu, 18 Dec 2014 16:21:54 GMT

←Older revision		Revision as of 16:21, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3l6b\| PDB=3l6b \| SCENE= }}~~	+	==X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor==
-	===X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor===	+	<StructureSection load='3l6b' size='340' side='right' caption='[[3l6b]], [[Resolution\|resolution]] 1.50Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20106978}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3l6b]] is a 1 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=3L6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L6B FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3l6c\|3l6c]], [[3l6r\|3l6r]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SRR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine_racemase Serine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.18 5.1.1.18] </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=3l6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l6b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3l6b RCSB], [http://www.ebi.ac.uk/pdbsum/3l6b 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/l6/3l6b_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 ==
		+	Serine racemase is responsible for the synthesis of D-serine, an endogenous co-agonist for N-methyl-D-aspartate receptor-type glutamate receptors (NMDARs). This pyridoxal 5'-phosphate-dependent enzyme is involved both in the reversible conversion of L- to D-serine and serine catabolism by alpha,beta-elimination of water, thereby regulating D-serine levels. Because D-serine affects NMDAR signaling throughout the brain, serine racemase is a promising target for the treatment of disorders related to NMDAR dysfunction. To provide a molecular basis for rational drug design the x-ray crystal structures of human and rat serine racemase were determined at 1.5- and 2.1-A resolution, respectively, and in the presence and absence of the orthosteric inhibitor malonate. The structures revealed a fold typical of beta-family pyridoxal 5'-phosphate enzymes, with both a large domain and a flexible small domain associated into a symmetric dimer, and indicated a ligand-induced rearrangement of the small domain that organizes the active site for specific turnover of the substrate.

-	~~==Function==~~	+	The structure of mammalian serine racemase: evidence for conformational changes upon inhibitor binding.,Smith MA, Mack V, Ebneth A, Moraes I, Felicetti B, Wood M, Schonfeld D, Mather O, Cesura A, Barker J J Biol Chem. 2010 Apr 23;285(17):12873-81. Epub 2010 Jan 27. PMID:20106978<ref>PMID:20106978</ref>
-	~~[[http://www.uniprot.org/uniprot/SRR_HUMAN SRR_HUMAN]] Catalyzes the synthesis~~ of ~~D-serine from L-~~serine. D~~-serine is a key coagonist with glutamate at NMDA receptors~~. ~~Has dehydratase activity towards both L~~-~~serine and D-serine~~.~~<ref>~~PMID:~~11054547</ref>~~ <ref>PMID:20106978</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3l6b]] is~~ a ~~1 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=3L6B OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:020106978</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Serine racemase]]		[[Category: Serine racemase]]
-	[[Category: Barker, J.]]	+	[[Category: Barker, J]]
-	[[Category: Cesura, A.]]	+	[[Category: Cesura, A]]
-	[[Category: Ebneth, A.]]	+	[[Category: Ebneth, A]]
-	[[Category: Felicetti, B.]]	+	[[Category: Felicetti, B]]
-	[[Category: Mack, V.]]	+	[[Category: Mack, V]]
-	[[Category: Moraes, I.]]	+	[[Category: Moraes, I]]
-	[[Category: Smith, M A.]]	+	[[Category: Smith, M A]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Plp]]		[[Category: Plp]]
	[[Category: Pyridoxal phosphate]]		[[Category: Pyridoxal phosphate]]
-	[[Category: Serine racemase]]

OCA: Protected "3l6b" [edit=sysop:move=sysop]

OCA — Thu, 04 Apr 2013 20:21:02 GMT

Protected "3l6b" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:21, 4 April 2013

OCA at 20:20, 4 April 2013

OCA — Thu, 04 Apr 2013 20:20:56 GMT

←Older revision		Revision as of 20:20, 4 April 2013
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-	{{Seed}}
-	[[Image:3l6b.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3l6b", 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_3l6b\| PDB=3l6b \| SCENE= }}		{{STRUCTURE_3l6b\| PDB=3l6b \| SCENE= }}
-
	===X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor===		===X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor===
		+	{{ABSTRACT_PUBMED_20106978}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/SRR_HUMAN SRR_HUMAN]] Catalyzes the synthesis of D-serine from L-serine. D-serine is a key coagonist with glutamate at NMDA receptors. Has dehydratase activity towards both L-serine and D-serine.<ref>PMID:11054547</ref> <ref>PMID:20106978</ref>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_20106978}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov), where 20106978 is~~ the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_20106978}}~~	+

	==About this Structure==		==About this Structure==
-	~~3L6B~~ is a 1 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=3L6B OCA].	+	[[3l6b]] is a 1 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=3L6B OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20106978~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020106978</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Serine racemase]]		[[Category: Serine racemase]]
Line 37:		Line 24:
	[[Category: Pyridoxal phosphate]]		[[Category: Pyridoxal phosphate]]
	[[Category: Serine racemase]]		[[Category: Serine racemase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 12 10:27:09 2010''

OCA at 07:27, 12 May 2010

OCA — Wed, 12 May 2010 07:27:09 GMT

←Older revision		Revision as of 07:27, 12 May 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3l6b.~~jpg~~\|left\|200px]]	+	[[Image:3l6b.png\|left\|200px]]

	<!--		<!--
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	===X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor===		===X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20106978}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20106978 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20106978}}

	==About this Structure==		==About this Structure==
	3L6B is a 1 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=3L6B OCA].		3L6B is a 1 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=3L6B OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20106978</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Serine racemase]]		[[Category: Serine racemase]]
-	[[Category: Barker, J J.]]	+	[[Category: Barker, J.]]
	[[Category: Cesura, A.]]		[[Category: Cesura, A.]]
	[[Category: Ebneth, A.]]		[[Category: Ebneth, A.]]
Line 29:		Line 38:
	[[Category: Serine racemase]]		[[Category: Serine racemase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jan 27 20~~:07:49 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 12 10:27:09 2010''

OCA at 18:07, 27 January 2010

OCA — Wed, 27 Jan 2010 18:07:50 GMT

←Older revision		Revision as of 18:07, 27 January 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3l6b.jpg\|left\|200px]]

-	The ~~entry 3l6b~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3l6b", 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_3l6b\| PDB=3l6b \| SCENE= }}

-	~~Authors: Smith, M.A., Barker, J.J., Mack, V., Ebneth, A., Moraes, I., Felicetti, B., Cesura, A.~~	+	===X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor===

-	Description: X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan ~~13 13~~:33:56 2010''	+	==About this Structure==
		+	3L6B is a 1 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=3L6B OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Serine racemase]]
		+	[[Category: Barker, J J.]]
		+	[[Category: Cesura, A.]]
		+	[[Category: Ebneth, A.]]
		+	[[Category: Felicetti, B.]]
		+	[[Category: Mack, V.]]
		+	[[Category: Moraes, I.]]
		+	[[Category: Smith, M A.]]
		+	[[Category: Isomerase]]
		+	[[Category: Plp]]
		+	[[Category: Pyridoxal phosphate]]
		+	[[Category: Serine racemase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 27 20:07:49 2010''