3dl0 - Revision history

OCA at 12:48, 30 August 2023

2023-08-30T12:48:22Z

←Older revision		Revision as of 12:48, 30 August 2023
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	<StructureSection load='3dl0' size='340' side='right'caption='[[3dl0]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='3dl0' size='340' side='right'caption='[[3dl0]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dl0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DL0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dl0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DL0 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AP5:BIS(ADENOSINE)~~-~~5-PENTAPHOSPHATE'>AP5</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.58Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3dkv\|3dkv]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ADK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1423~~ "~~Bacillus globigii~~" ~~Migula 1900])~~<~~/td~~></tr>	+
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3]~~ </~~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=3dl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl0 OCA], [https://pdbe.org/3dl0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dl0 RCSB], [https://www.ebi.ac.uk/pdbsum/3dl0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dl0 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=3dl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl0 OCA], [https://pdbe.org/3dl0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dl0 RCSB], [https://www.ebi.ac.uk/pdbsum/3dl0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dl0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/KAD_BACSU KAD_BACSU]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth.	+	[https://www.uniprot.org/uniprot/KAD_BACSU KAD_BACSU] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth.
	== 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: Bacillus ~~globigii migula 1900]]~~	+	[[Category: Bacillus subtilis]]
-	~~[[Category: Adenylate kinase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bannen~~, R M~~]]	+	[[Category: Bannen RM]]
-	[[Category: Bianchetti~~, C M~~]]	+	[[Category: Bianchetti CM]]
-	[[Category: Bingman~~, C A~~]]	+	[[Category: Bingman CA]]
-	[[Category: McCoy~~, J G]]~~	+	[[Category: McCoy JG]]
-	~~[[Category: Atp-binding]]~~	+
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nucleotide biosynthesis]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Phosphotransferase]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Zinc coordination~~]]	+

OCA at 08:01, 9 February 2022

2022-02-09T08:01:24Z

←Older revision		Revision as of 08:01, 9 February 2022
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	==Crystal structure of adenylate kinase variant AKlse3==		==Crystal structure of adenylate kinase variant AKlse3==
-	<StructureSection load='3dl0' size='340' side='right' caption='[[3dl0]], [[Resolution\|resolution]] 1.58Å' scene=''>	+	<StructureSection load='3dl0' size='340' side='right'caption='[[3dl0]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dl0]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DL0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dl0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DL0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dkv\|3dkv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dkv\|3dkv]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=3dl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl0 OCA], [~~http~~://pdbe.org/3dl0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dl0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dl0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dl0 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=3dl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl0 OCA], [https://pdbe.org/3dl0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dl0 RCSB], [https://www.ebi.ac.uk/pdbsum/3dl0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dl0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/KAD_BACSU KAD_BACSU]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth.	+	[[https://www.uniprot.org/uniprot/KAD_BACSU KAD_BACSU]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/3dl0_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dl/3dl0_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 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 3dl0" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3dl0" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Adenylate kinase 3D structures\|Adenylate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 40:
	[[Category: Bacillus globigii migula 1900]]		[[Category: Bacillus globigii migula 1900]]
	[[Category: Adenylate kinase]]		[[Category: Adenylate kinase]]
		+	[[Category: Large Structures]]
	[[Category: Bannen, R M]]		[[Category: Bannen, R M]]
	[[Category: Bianchetti, C M]]		[[Category: Bianchetti, C M]]

OCA at 08:52, 25 October 2017

2017-10-25T08:52:24Z

←Older revision		Revision as of 08:52, 25 October 2017
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 3dl0" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3dl0" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Adenylate kinase\|Adenylate kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:03, 5 August 2016

2016-08-05T11:03:42Z

←Older revision		Revision as of 11:03, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of adenylate kinase variant AKlse3==		==Crystal structure of adenylate kinase variant AKlse3==
	<StructureSection load='3dl0' size='340' side='right' caption='[[3dl0]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='3dl0' size='340' side='right' caption='[[3dl0]], [[Resolution\|resolution]] 1.58Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=3dl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dl0 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl0 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=3dl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl0 OCA], [http://pdbe.org/3dl0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dl0 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dl0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=3dl0 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 3dl0" style="background-color:#fffaf0;"></div>

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

OCA at 18:16, 25 December 2014

2014-12-25T18:16:30Z

←Older revision		Revision as of 18:16, 25 December 2014
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	<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=3dl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dl0 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl0 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=3dl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dl0 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl0 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KAD_BACSU KAD_BACSU]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		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>
		+
		+	==See Also==
		+	*[[Adenylate kinase\|Adenylate kinase]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 38:
	[[Category: Bacillus globigii migula 1900]]		[[Category: Bacillus globigii migula 1900]]
	[[Category: Adenylate kinase]]		[[Category: Adenylate kinase]]
-	[[Category: Bannen, R M.]]	+	[[Category: Bannen, R M]]
-	[[Category: Bianchetti, C M.]]	+	[[Category: Bianchetti, C M]]
-	[[Category: Bingman, C A.]]	+	[[Category: Bingman, C A]]
-	[[Category: McCoy, J G.]]	+	[[Category: McCoy, J G]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Kinase]]		[[Category: Kinase]]

OCA at 08:49, 20 October 2014

2014-10-20T08:49:35Z

←Older revision		Revision as of 08:49, 20 October 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dl0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DL0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dl0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DL0 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dkv\|3dkv]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dkv\|3dkv]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=3dl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dl0 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl0 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=3dl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dl0 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl0 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 27:		Line 27:
	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>
-
-	==See Also==
-	*[[Adenylate kinase\|Adenylate kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:21, 25 June 2014

2014-06-25T05:21:26Z

←Older revision		Revision as of 05:21, 25 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3dl0.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of adenylate kinase variant AKlse3==
		+	<StructureSection load='3dl0' size='340' side='right' caption='[[3dl0]], [[Resolution\|resolution]] 1.58Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3dl0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DL0 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dkv\|3dkv]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=3dl0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dl0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dl0 RCSB], [http://www.ebi.ac.uk/pdbsum/3dl0 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/dl/3dl0_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 ==
		+	Local structural entropy (LSE) is a descriptor for the extent of conformational heterogeneity in short protein sequences that is computed from structural information derived from the Protein Data Bank. Reducing the LSE of a protein sequence by introducing amino acid mutations can result in fewer conformational states and thus a more stable structure, indicating that LSE optimization can be used as a protein stabilization method. Here, we describe a series of LSE optimization experiments designed to stabilize mesophilic and thermophilic adenylate kinases (AKs) and report crystal structures of LSE-optimized AK variants. In the mesophilic AK, thermal stabilization by LSE reduction was effective but limited. Structural analyses of the LSE-optimized mesophilic AK variants revealed a strong correlation between LSE and the apolar buried surface area. Additional mutations designed to introduce non-covalent interactions between distant regions of the polypeptide resulted in further stabilization. Unexpectedly, optimizing the LSE of the thermophilic AK resulted in a decrease in thermal stability. This destabilization was reduced when charged residues were excluded from the possible substitutions during LSE optimization. These observations suggest that stabilization by LSE reduction may result from the optimization of local hydrophobic contacts. The limitations of this process are likely due to ignorance of other interactions that bridge distant regions in a given amino acid sequence. Our results illustrate the effectiveness and limitations of LSE optimization as a protein stabilization strategy and highlight the importance and complementarity of local conformational stability and global interactions in protein thermal stability. (c) Proteins 2014;. (c) 2014 Wiley Periodicals, Inc.

-	~~{{STRUCTURE_3dl0\| PDB=3dl0 \| SCENE= }}~~	+	Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases.,Moon S, Bannen RM, Rutkoski TJ, Phillips GN Jr, Bae E Proteins. 2014 Jun 13. doi: 10.1002/prot.24627. PMID:24931334<ref>PMID:24931334</ref>

-	~~===Crystal structure~~ of ~~adenylate kinase variant AKlse3===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+
-	~~==About this Structure==~~	+
-	~~[[3dl0]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_subtilis Bacillus subtilis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3DL0 OCA].~~	+

	==See Also==		==See Also==
	*[[Adenylate kinase\|Adenylate kinase]]		*[[Adenylate kinase\|Adenylate kinase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Adenylate kinase]]		[[Category: Adenylate kinase]]
-	[[Category: Bacillus subtilis]]
	[[Category: Bannen, R M.]]		[[Category: Bannen, R M.]]
	[[Category: Bianchetti, C M.]]		[[Category: Bianchetti, C M.]]

OCA at 06:38, 24 October 2012

2012-10-24T06:38:57Z

←Older revision		Revision as of 06:38, 24 October 2012
Line 15:		Line 15:
	[[Category: Bannen, R M.]]		[[Category: Bannen, R M.]]
	[[Category: Bianchetti, C M.]]		[[Category: Bianchetti, C M.]]
-	[[Category: Bingman, C B.]]	+	[[Category: Bingman, C A.]]
	[[Category: McCoy, J G.]]		[[Category: McCoy, J G.]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]

OCA at 19:52, 20 October 2012

2012-10-20T19:52:33Z

←Older revision		Revision as of 19:52, 20 October 2012
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[3dl0]] is a 2 chain structure ~~of [[Adenylate kinase]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL0 OCA].	+	[[3dl0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DL0 OCA].

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

OCA: Protected "3dl0" [edit=sysop:move=sysop]

2012-07-27T08:45:36Z

Protected "3dl0" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:45, 27 July 2012