1d7k - Revision history

OCA at 15:47, 13 March 2024

OCA — Wed, 13 Mar 2024 15:47:01 GMT

←Older revision		Revision as of 15:47, 13 March 2024
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	<StructureSection load='1d7k' size='340' side='right'caption='[[1d7k]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1d7k' size='340' side='right'caption='[[1d7k]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1d7k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D7K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1d7k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D7K FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=LLP:(2S)-2-AMINO-6~~-[[~~3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL~~]~~METHYLIDENEAMINO~~]~~HEXANOIC+ACID'>LLP</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='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number~~ [~~https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=~~4~~.1.1.17 4.1.1.17~~] </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</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=1d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7k OCA], [https://pdbe.org/1d7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d7k RCSB], [https://www.ebi.ac.uk/pdbsum/1d7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7k 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=1d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7k OCA], [https://pdbe.org/1d7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d7k RCSB], [https://www.ebi.ac.uk/pdbsum/1d7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7k ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DCOR_HUMAN DCOR_HUMAN]
	== 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=1d7k 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=1d7k ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The polyamines spermidine and spermine are ubiquitous and required for cell growth and differentiation in eukaryotes. Ornithine decarboxylase (ODC, EC 4.1.1.17) performs the first step in polyamine biosynthesis, the decarboxylation of ornithine to putrescine. Elevated polyamine levels can lead to down-regulation of ODC activity by enhancing the translation of antizyme mRNA, resulting in subsequent binding of antizyme to ODC monomers which targets ODC for proteolysis by the 26S proteasome.The crystal structure of ornithine decarboxylase from human liver has been determined to 2.1 A resolution by molecular replacement using truncated mouse ODC (Delta425-461) as the search model and refined to a crystallographic R-factor of 21.2% and an R-free value of 28.8%. The human ODC model includes several regions that are disordered in the mouse ODC crystal structure, including one of two C-terminal basal degradation elements that have been demonstrated to independently collaborate with antizyme binding to target ODC for degradation by the 26S proteasome.The crystal structure of human ODC suggests that the C terminus, which contains basal degradation elements necessary for antizyme-induced proteolysis, is not buried by the structural core of homodimeric ODC as previously proposed. Analysis of the solvent-accessible surface area, surface electrostatic potential, and the conservation of primary sequence between human ODC and Trypanosoma brucei ODC provides clues to the identity of potential protein-binding-determinants in the putative antizyme binding element in human ODC.
-
-	Crystal structure of human ornithine decarboxylase at 2.1 A resolution: structural insights to antizyme binding.,Almrud JJ, Oliveira MA, Kern AD, Grishin NV, Phillips MA, Hackert ML J Mol Biol. 2000 Jan 7;295(1):7-16. PMID:10623504<ref>PMID:10623504</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1d7k" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ornithine decarboxylase\|Ornithine decarboxylase]]		*[[Ornithine decarboxylase\|Ornithine decarboxylase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Ornithine decarboxylase]]~~	+	[[Category: Almrud JJ]]
-	[[Category: Almrud~~, J J~~]]	+	[[Category: Grishin NV]]
-	[[Category: Grishin~~, N V~~]]	+	[[Category: Hackert ML]]
-	[[Category: Hackert~~, M L~~]]	+	[[Category: Kern AD]]
-	[[Category: Kern~~, A D~~]]	+	[[Category: Oliveira MA]]
-	[[Category: Oliveira~~, M A~~]]	+	[[Category: Phillips MA]]
-	[[Category: Phillips~~, M A]]~~	+
-	~~[[Category: Alpha-beta barrel]]~~	+
-	~~[[Category: Decarboxylation]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Ornithine]]~~	+
-	~~[[Category: Pyridoxal 5'-phosphate]]~~	+
-	~~[[Category: Sheet-domain~~]]	+

OCA at 06:30, 11 August 2021

OCA — Wed, 11 Aug 2021 06:30:07 GMT

←Older revision		Revision as of 06:30, 11 August 2021
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	<StructureSection load='1d7k' size='340' side='right'caption='[[1d7k]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1d7k' size='340' side='right'caption='[[1d7k]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1d7k]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1D7K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1d7k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D7K FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </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=1d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7k OCA], [~~http~~://pdbe.org/1d7k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1d7k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1d7k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7k 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=1d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7k OCA], [https://pdbe.org/1d7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d7k RCSB], [https://www.ebi.ac.uk/pdbsum/1d7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7k ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 09:38, 6 November 2019

OCA — Wed, 06 Nov 2019 09:38:45 GMT

←Older revision		Revision as of 09:38, 6 November 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION==		==CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION==
-	<StructureSection load='1d7k' size='340' side='right' caption='[[1d7k]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1d7k' size='340' side='right'caption='[[1d7k]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1d7k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7K FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d7k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7K FirstGlance]. <br>
Line 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1d7k" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1d7k" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ornithine decarboxylase\|Ornithine decarboxylase]]
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Ornithine decarboxylase]]		[[Category: Ornithine decarboxylase]]
	[[Category: Almrud, J J]]		[[Category: Almrud, J J]]

OCA at 08:31, 6 December 2017

OCA — Wed, 06 Dec 2017 08:31:06 GMT

←Older revision		Revision as of 08:31, 6 December 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION==		==CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION==
	<StructureSection load='1d7k' size='340' side='right' caption='[[1d7k]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1d7k' size='340' side='right' caption='[[1d7k]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </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=1d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7k OCA], [http://pdbe.org/1d7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d7k RCSB], [http://www.ebi.ac.uk/pdbsum/1d7k 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=1d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7k OCA], [http://pdbe.org/1d7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d7k RCSB], [http://www.ebi.ac.uk/pdbsum/1d7k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1d7k ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d7/1d7k_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d7/1d7k_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 26:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1d7k" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1d7k" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ornithine decarboxylase\|Ornithine decarboxylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:09, 9 February 2016

OCA — Tue, 09 Feb 2016 21:09:55 GMT

←Older revision		Revision as of 21:09, 9 February 2016
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1d7k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7K FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d7k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7K FirstGlance]. <br>
-	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-~~LYSINE(~~3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-~~YLMETHANE)~~'>LLP</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </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=1d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7k OCA], [http://pdbe.org/1d7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d7k RCSB], [http://www.ebi.ac.uk/pdbsum/1d7k 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=1d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7k OCA], [http://pdbe.org/1d7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d7k RCSB], [http://www.ebi.ac.uk/pdbsum/1d7k PDBsum]</span></td></tr>
Line 15:		Line 15:
	<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=1d7k ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:03, 11 September 2015

OCA — Fri, 11 Sep 2015 02:03:58 GMT

←Older revision		Revision as of 02:03, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1d7k' size='340' side='right' caption='[[1d7k]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1d7k' size='340' side='right' caption='[[1d7k]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1d7k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1d7k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7K FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </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=1d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d7k RCSB], [http://www.ebi.ac.uk/pdbsum/1d7k 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=1d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7k OCA], [http://pdbe.org/1d7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d7k RCSB], [http://www.ebi.ac.uk/pdbsum/1d7k PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1d7k" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Ornithine decarboxylase]]		[[Category: Ornithine decarboxylase]]
	[[Category: Almrud, J J]]		[[Category: Almrud, J J]]

OCA at 22:21, 22 December 2014

OCA — Mon, 22 Dec 2014 22:21:08 GMT

←Older revision		Revision as of 22:21, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1d7k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7K FirstGlance]. <br>		<table><tr><td colspan='2'>[[1d7k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7K FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </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=1d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d7k RCSB], [http://www.ebi.ac.uk/pdbsum/1d7k 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=1d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d7k RCSB], [http://www.ebi.ac.uk/pdbsum/1d7k 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 34:		Line 34:
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Ornithine decarboxylase]]		[[Category: Ornithine decarboxylase]]
-	[[Category: Almrud, J J.]]	+	[[Category: Almrud, J J]]
-	[[Category: Grishin, N V.]]	+	[[Category: Grishin, N V]]
-	[[Category: Hackert, M L.]]	+	[[Category: Hackert, M L]]
-	[[Category: Kern, A D.]]	+	[[Category: Kern, A D]]
-	[[Category: Oliveira, M A.]]	+	[[Category: Oliveira, M A]]
-	[[Category: Phillips, M A.]]	+	[[Category: Phillips, M A]]
	[[Category: Alpha-beta barrel]]		[[Category: Alpha-beta barrel]]
	[[Category: Decarboxylation]]		[[Category: Decarboxylation]]

OCA at 16:11, 29 September 2014

OCA — Mon, 29 Sep 2014 16:11:17 GMT

←Older revision		Revision as of 16:11, 29 September 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1d7k\| PDB=1d7k \| SCENE= }}~~	+	==CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION==
-	===CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION===	+	<StructureSection load='1d7k' size='340' side='right' caption='[[1d7k]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_10623504}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1d7k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D7K FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)'>LLP</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ornithine_decarboxylase Ornithine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.17 4.1.1.17] </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=1d7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d7k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d7k RCSB], [http://www.ebi.ac.uk/pdbsum/1d7k 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/d7/1d7k_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 polyamines spermidine and spermine are ubiquitous and required for cell growth and differentiation in eukaryotes. Ornithine decarboxylase (ODC, EC 4.1.1.17) performs the first step in polyamine biosynthesis, the decarboxylation of ornithine to putrescine. Elevated polyamine levels can lead to down-regulation of ODC activity by enhancing the translation of antizyme mRNA, resulting in subsequent binding of antizyme to ODC monomers which targets ODC for proteolysis by the 26S proteasome.The crystal structure of ornithine decarboxylase from human liver has been determined to 2.1 A resolution by molecular replacement using truncated mouse ODC (Delta425-461) as the search model and refined to a crystallographic R-factor of 21.2% and an R-free value of 28.8%. The human ODC model includes several regions that are disordered in the mouse ODC crystal structure, including one of two C-terminal basal degradation elements that have been demonstrated to independently collaborate with antizyme binding to target ODC for degradation by the 26S proteasome.The crystal structure of human ODC suggests that the C terminus, which contains basal degradation elements necessary for antizyme-induced proteolysis, is not buried by the structural core of homodimeric ODC as previously proposed. Analysis of the solvent-accessible surface area, surface electrostatic potential, and the conservation of primary sequence between human ODC and Trypanosoma brucei ODC provides clues to the identity of potential protein-binding-determinants in the putative antizyme binding element in human ODC.

-	~~==About this Structure==~~	+	Crystal structure of human ornithine decarboxylase at 2.1 A resolution: structural insights to antizyme binding.,Almrud JJ, Oliveira MA, Kern AD, Grishin NV, Phillips MA, Hackert ML J Mol Biol. 2000 Jan 7;295(1):7-16. PMID:10623504<ref>PMID:10623504</ref>
-	~~[[1d7k]] is a~~ 2 ~~chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=1D7K OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Ornithine decarboxylase\|Ornithine decarboxylase]]		*[[Ornithine decarboxylase\|Ornithine decarboxylase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010623504<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Ornithine decarboxylase]]		[[Category: Ornithine decarboxylase]]

OCA at 09:32, 11 March 2013

OCA — Mon, 11 Mar 2013 09:32:31 GMT

←Older revision		Revision as of 09:32, 11 March 2013
Line 1:		Line 1:
-	[[Image:1d7k.png\|left\|200px]]
-
	{{STRUCTURE_1d7k\| PDB=1d7k \| SCENE= }}		{{STRUCTURE_1d7k\| PDB=1d7k \| SCENE= }}
-
	===CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION===		===CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION===
-
	{{ABSTRACT_PUBMED_10623504}}		{{ABSTRACT_PUBMED_10623504}}

OCA: Protected "1d7k" [edit=sysop:move=sysop]

OCA — Sun, 21 Oct 2012 20:45:27 GMT

Protected "1d7k" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:45, 21 October 2012