3dpp - Revision history

OCA at 05:46, 17 October 2024

2024-10-17T05:46:12Z

← Older revision		Revision as of 05:46, 17 October 2024
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dp/3dpp_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dp/3dpp_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 12:50, 30 August 2023

2023-08-30T12:50:54Z

← Older revision		Revision as of 12:50, 30 August 2023
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	<StructureSection load='3dpp' size='340' side='right'caption='[[3dpp]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3dpp' size='340' side='right'caption='[[3dpp]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dpp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DPP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dpp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Pyrrhocoris_apterus Pyrrhocoris apterus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DPP FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.5Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALC:2-AMINO-3-CYCLOHEXYL-PROPIONIC+ACID'>ALC</scene><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALC:2-AMINO-3-CYCLOHEXYL-PROPIONIC+ACID'>ALC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[3dpo\|3dpo]], [[3dpq\|3dpq]]~~</~~div></td></tr>~~
	~~<tr id='gene'~~><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaK, groP, grpF, seg, b0014, JW0013 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3dpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpp OCA], [https://pdbe.org/3dpp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dpp RCSB], [https://www.ebi.ac.uk/pdbsum/3dpp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpp 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=3dpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpp OCA], [https://pdbe.org/3dpp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dpp RCSB], [https://www.ebi.ac.uk/pdbsum/3dpp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/DNAK_ECOLI DNAK_ECOLI]] Plays an essential role in the initiation of phage lambda DNA replication, where it acts in an ATP-dependent fashion with the DnaJ protein to release lambda O and P proteins from the preprimosomal complex. DnaK is also involved in chromosomal DNA replication, possibly through an analogous interaction with the DnaA protein. Also participates actively in the response to hyperosmotic shock.[HAMAP-Rule:MF_00332]		[https://www.uniprot.org/uniprot/DNAK_ECOLI DNAK_ECOLI] Plays an essential role in the initiation of phage lambda DNA replication, where it acts in an ATP-dependent fashion with the DnaJ protein to release lambda O and P proteins from the preprimosomal complex. DnaK is also involved in chromosomal DNA replication, possibly through an analogous interaction with the DnaA protein. Also participates actively in the response to hyperosmotic shock.[HAMAP-Rule:MF_00332]
	== 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: ~~Ecoli~~]]		[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Roujeinikova, A~~]]		[[Category: Pyrrhocoris apterus]]
	[[Category: ~~Atp-binding]]~~		[[Category: Roujeinikova A]]
	~~[[Category: Chaperone]]~~
	~~[[Category: Cytoplasm]]~~
	~~[[Category: Dna replication]]~~
	~~[[Category: Dnak]]~~
	~~[[Category: Hsp70]]~~
	~~[[Category: Membrane]]~~
	~~[[Category: Molecular chaperone]]~~
	~~[[Category: Nucleotide-binding]]~~
	~~[[Category: Peptide binding protein]]~~
	~~[[Category: Phosphoprotein]]~~
	~~[[Category: Pyrrhocoricin inhibitor]]~~
	~~[[Category: Stress response]]~~
	~~[[Category: Substrate-binding domain~~]]

OCA at 08:05, 9 February 2022

2022-02-09T08:05:07Z

← Older revision		Revision as of 08:05, 9 February 2022
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	==Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form A)==		==Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form A)==
	<StructureSection load='3dpp' size='340' side='right' caption='[[3dpp]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3dpp' size='340' side='right'caption='[[3dpp]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dpp]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DPP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dpp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DPP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALC:2-AMINO-3-CYCLOHEXYL-PROPIONIC+ACID'>ALC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALC:2-AMINO-3-CYCLOHEXYL-PROPIONIC+ACID'>ALC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dpo\|3dpo]], [[3dpq\|3dpq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dpo\|3dpo]], [[3dpq\|3dpq]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaK, groP, grpF, seg, b0014, JW0013 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaK, groP, grpF, seg, b0014, JW0013 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3dpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpp OCA], [~~http~~://pdbe.org/3dpp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dpp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dpp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpp 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=3dpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpp OCA], [https://pdbe.org/3dpp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dpp RCSB], [https://www.ebi.ac.uk/pdbsum/3dpp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/DNAK_ECOLI DNAK_ECOLI]] Plays an essential role in the initiation of phage lambda DNA replication, where it acts in an ATP-dependent fashion with the DnaJ protein to release lambda O and P proteins from the preprimosomal complex. DnaK is also involved in chromosomal DNA replication, possibly through an analogous interaction with the DnaA protein. Also participates actively in the response to hyperosmotic shock.[HAMAP-Rule:MF_00332]		[[https://www.uniprot.org/uniprot/DNAK_ECOLI DNAK_ECOLI]] Plays an essential role in the initiation of phage lambda DNA replication, where it acts in an ATP-dependent fashion with the DnaJ protein to release lambda O and P proteins from the preprimosomal complex. DnaK is also involved in chromosomal DNA replication, possibly through an analogous interaction with the DnaA protein. Also participates actively in the response to hyperosmotic shock.[HAMAP-Rule:MF_00332]
	== 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/dp/3dpp_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dp/3dpp_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>
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	</div>		</div>
	<div class="pdbe-citations 3dpp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3dpp" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Heat Shock Protein structures\|Heat Shock Protein structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
			[[Category: Large Structures]]
	[[Category: Roujeinikova, A]]		[[Category: Roujeinikova, A]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]

OCA at 08:54, 25 October 2017

2017-10-25T08:54:47Z

← Older revision		Revision as of 08:54, 25 October 2017
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	</div>		</div>
	<div class="pdbe-citations 3dpp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3dpp" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[Heat Shock Proteins\|Heat Shock Proteins]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Chaperone]]		[[Category: Chaperone]]
			[[Category: Cytoplasm]]
	[[Category: Dna replication]]		[[Category: Dna replication]]
	[[Category: Dnak]]		[[Category: Dnak]]

OCA at 22:48, 5 August 2016

2016-08-05T22:48:32Z

← Older revision		Revision as of 22:48, 5 August 2016
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	==Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form A)==		==Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form A)==
	<StructureSection load='3dpp' size='340' side='right' caption='[[3dpp]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='3dpp' size='340' side='right' caption='[[3dpp]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dpp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia coli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dpp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALC:2-AMINO-3-CYCLOHEXYL-PROPIONIC+ACID'>ALC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALC:2-AMINO-3-CYCLOHEXYL-PROPIONIC+ACID'>ALC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dpo\|3dpo]], [[3dpq\|3dpq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dpo\|3dpo]], [[3dpq\|3dpq]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaK, groP, grpF, seg, b0014, JW0013 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~562 Escherichia coli~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaK, groP, grpF, seg, b0014, JW0013 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3dpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dpp RCSB], [http://www.ebi.ac.uk/pdbsum/3dpp 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=3dpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpp OCA], [http://pdbe.org/3dpp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dpp RCSB], [http://www.ebi.ac.uk/pdbsum/3dpp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpp 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=3dpp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	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 3dpp" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia coli~~]]		[[Category: Ecoli]]
	[[Category: Roujeinikova, A]]		[[Category: Roujeinikova, A]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]

OCA at 22:36, 25 December 2014

2014-12-25T22:36:22Z

← Older revision		Revision as of 22:36, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dpp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dpp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPP FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALC:2-AMINO-3-CYCLOHEXYL-PROPIONIC+ACID'>ALC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALC:2-AMINO-3-CYCLOHEXYL-PROPIONIC+ACID'>ALC</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dpo\|3dpo]], [[3dpq\|3dpq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dpo\|3dpo]], [[3dpq\|3dpq]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaK, groP, grpF, seg, b0014, JW0013 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaK, groP, grpF, seg, b0014, JW0013 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3dpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dpp RCSB], [http://www.ebi.ac.uk/pdbsum/3dpp 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=3dpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dpp RCSB], [http://www.ebi.ac.uk/pdbsum/3dpp PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/DNAK_ECOLI DNAK_ECOLI]] Plays an essential role in the initiation of phage lambda DNA replication, where it acts in an ATP-dependent fashion with the DnaJ protein to release lambda O and P proteins from the preprimosomal complex. DnaK is also involved in chromosomal DNA replication, possibly through an analogous interaction with the DnaA protein. Also participates actively in the response to hyperosmotic shock.[HAMAP-Rule:MF_00332]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Roujeinikova, A.]]		[[Category: Roujeinikova, A]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Chaperone]]		[[Category: Chaperone]]

OCA at 13:08, 29 September 2014

2014-09-29T13:08:59Z

← Older revision		Revision as of 13:08, 29 September 2014
Line 1:		Line 1:
	[[Image:~~3dpp~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form A)==
			<StructureSection load='3dpp' size='340' side='right' caption='[[3dpp]], [[Resolution\|resolution]] 2.50Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3dpp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPP FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
			<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALC:2-AMINO-3-CYCLOHEXYL-PROPIONIC+ACID'>ALC</scene></td></tr>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dpo\|3dpo]], [[3dpq\|3dpq]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dnaK, groP, grpF, seg, b0014, JW0013 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3dpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dpp RCSB], [http://www.ebi.ac.uk/pdbsum/3dpp 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/dp/3dpp_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 molecular chaperone DnaK assists protein folding and refolding, translocation across membranes, and regulation of the heat shock response. In Escherichia coli, the protein is a target for insect-derived antimicrobial peptides, pyrrhocoricins. We present here the X-ray crystallographic analysis of the E. coli DnaK substrate-binding domain in complex with pyrrhocoricin-derived peptide inhibitors. The structures show that pyrrhocoricins act as site-specific, dual-mode (competitive and allosteric) inhibitors, occupying the substrate-binding tunnel and disrupting the latch between the lid and the beta-sandwich. Our structural analysis revealed an allosteric coupling between the movements of the lid and the interdomain linker, identifying a previously unknown mechanism of the lid-mediated regulation of the chaperone cycle.

	~~{{STRUCTURE_3dpp\| PDB=3dpp \| SCENE= }}~~		Allosteric coupling between the lid and interdomain linker in DnaK revealed by inhibitor binding studies.,Liebscher M, Roujeinikova A J Bacteriol. 2009 Mar;191(5):1456-62. Epub 2008 Dec 19. PMID:19103929<ref>PMID:19103929</ref>

	~~===Crystal structure~~ of the ~~substrate binding domain~~ of E. ~~coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form A)===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_19103929}}~~

	~~==About this Structure==~~
	~~[[3dpp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il~~/~~oca-bin/ocashort?id=3DPP OCA].~~

	==See Also==		==See Also==
	*[[Heat Shock Proteins\|Heat Shock Proteins]]		*[[Heat Shock Proteins\|Heat Shock Proteins]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:019103929<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Roujeinikova, A.]]		[[Category: Roujeinikova, A.]]

OCA at 22:27, 20 October 2012

2012-10-20T22:27:46Z

← Older revision		Revision as of 22:27, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[3dpp]] is a 4 chain structure ~~of [[Heat Shock Proteins]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPP OCA].		[[3dpp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPP OCA].

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

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

2012-07-27T16:22:40Z

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

← Older revision	Revision as of 16:22, 27 July 2012
(No difference)

OCA at 16:22, 27 July 2012

2012-07-27T16:22:38Z

← Older revision		Revision as of 16:22, 27 July 2012
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	~~{{Seed}}~~
	[[Image:3dpp.png\|left\|200px]]		[[Image:3dpp.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3dpp", 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_3dpp\| PDB=3dpp \| SCENE= }}		{{STRUCTURE_3dpp\| PDB=3dpp \| SCENE= }}

	===Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form A)===		===Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form A)===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_19103929}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 19103929 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_19103929}}		{{ABSTRACT_PUBMED_19103929}}

	==About this Structure==		==About this Structure==
	~~3DPP~~ is a 4 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPP OCA].		[[3dpp]] is a 4 chain structure of [[Heat Shock Proteins]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPP OCA].

			==See Also==
			*[[Heat Shock Proteins\|Heat Shock Proteins]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~19103929~~</ref><references group="xtra"/>		<ref group="xtra">PMID:019103929</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Roujeinikova, A.]]		[[Category: Roujeinikova, A.]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Chaperone]]		[[Category: Chaperone]]
	~~[[Category: Cytoplasm]]~~
	[[Category: Dna replication]]		[[Category: Dna replication]]
	[[Category: Dnak]]		[[Category: Dnak]]
Line 40:		Line 30:
	[[Category: Stress response]]		[[Category: Stress response]]
	[[Category: Substrate-binding domain]]		[[Category: Substrate-binding domain]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 10 22:53:15 2009''~~