1vom - Revision history

OCA at 08:46, 14 February 2024

OCA — Wed, 14 Feb 2024 08:46:43 GMT

←Older revision		Revision as of 08:46, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1vom' size='340' side='right'caption='[[1vom]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1vom' size='340' side='right'caption='[[1vom]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1vom]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_11735 Atcc 11735~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VOM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1vom]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VOM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</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]] 1.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</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=1vom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vom OCA], [https://pdbe.org/1vom PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vom RCSB], [https://www.ebi.ac.uk/pdbsum/1vom PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vom 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=1vom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vom OCA], [https://pdbe.org/1vom PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vom RCSB], [https://www.ebi.ac.uk/pdbsum/1vom PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vom ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MYS2_DICDI MYS2_DICDI]] Myosin is a protein that binds to actin and has ATPase activity that is activated by actin.	+	[https://www.uniprot.org/uniprot/MYS2_DICDI MYS2_DICDI] Myosin is a protein that binds to actin and has ATPase activity that is activated by actin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</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=1vom 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=1vom ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The structure of the vanadate-trapped ADP complex of a truncated head of Dictyostelium myosin II consisting of residues Asp 2-Asn 762 has been determined by molecular replacement at 1.9 A resolution and refined to a crystallographic R-factor of 19.4%. The crystals belong to the orthorhombic space group C2221 where a = 84.50 A, b = 145.4 A, and c = 152.8 A. The conformation of the protein is similar to that of MgADP.AlF4.SlDc [Fisher, A.J., et al. (1995) Biochemistry 34, 8960-8972]. The nucleotide binding site contains a complex between MgADP and vanadate where MgADP exhibits a very similar conformation to that seen in previous complexes. The vanadate ion adopts a trigonal bipyramidal coordination. The three equatorial oxygen ligands are fairly short, average 1.7 A, relative to a single bond distance of approximately 1.8 A and are coordinated to the magnesium ion, N zeta of Lys 185, and five other protein ligands. The apical coordination to the vanadate ion is filled by a terminal oxygen on the beta-phosphate of ADP and a water molecule at bond distances of 2.1 and 2.3 A, respectively. The long length of the apical bonds suggests that the bond order is considerably less than unity. This structure confirms the earlier suggestion that vanadate is a model for the transition state of ATP hydrolysis and thus provides insight into those factors that are responsible for catalysis. In particular, it shows that the protein ligands and water structure surrounding the gamma-phosphate pocket are oriented to stabilize a water molecule in an appropriate position for in-line nucleophilic attack on the gamma-phosphorus of ATP. This structure reveals also an orientation of the COOH-terminal region beyond Thr 688 which is very different from that observed in either MgADP.BeFx.SlDc or chicken skeletal myosin subfragment 1. This is consistent with the COOH-terminal region of the molecule playing an important role in the transduction of chemical energy of hydrolysis of ATP into mechanical movement.
-
-	X-ray structure of the magnesium(II).ADP.vanadate complex of the Dictyostelium discoideum myosin motor domain to 1.9 A resolution.,Smith CA, Rayment I Biochemistry. 1996 Apr 30;35(17):5404-17. PMID:8611530<ref>PMID:8611530</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1vom" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Myosin 3D Structures\|Myosin 3D Structures]]		*[[Myosin 3D Structures\|Myosin 3D Structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 11735~~]]	+	[[Category: Dictyostelium discoideum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Rayment, I]]	+	[[Category: Rayment I]]
-	[[Category: Smith~~, C A]]~~	+	[[Category: Smith CA]]
-	~~[[Category: Molecular motor]]~~	+
-	~~[[Category: Muscle protein]]~~	+
-	~~[[Category: Myosin]]~~	+
-	~~[[Category: Transition-state analog~~]]	+

OCA at 13:24, 13 October 2021

OCA — Wed, 13 Oct 2021 13:24:59 GMT

←Older revision		Revision as of 13:24, 13 October 2021
Line 3:		Line 3:
	<StructureSection load='1vom' size='340' side='right'caption='[[1vom]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1vom' size='340' side='right'caption='[[1vom]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1vom]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1VOM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1vom]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VOM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></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=1vom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vom OCA], [~~http~~://pdbe.org/1vom PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1vom RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1vom PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1vom 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=1vom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vom OCA], [https://pdbe.org/1vom PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vom RCSB], [https://www.ebi.ac.uk/pdbsum/1vom PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vom ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MYS2_DICDI MYS2_DICDI]] Myosin is a protein that binds to actin and has ATPase activity that is activated by actin.	+	[[https://www.uniprot.org/uniprot/MYS2_DICDI MYS2_DICDI]] Myosin is a protein that binds to actin and has ATPase activity that is activated by actin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:19, 8 January 2020

OCA — Wed, 08 Jan 2020 10:19:51 GMT

←Older revision		Revision as of 10:19, 8 January 2020
Line 1:		Line 1:

	==COMPLEX BETWEEN DICTYOSTELIUM MYOSIN AND MGADP AND VANADATE AT 1.9A RESOLUTION==		==COMPLEX BETWEEN DICTYOSTELIUM MYOSIN AND MGADP AND VANADATE AT 1.9A RESOLUTION==
-	<StructureSection load='1vom' size='340' side='right' caption='[[1vom]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1vom' size='340' side='right'caption='[[1vom]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1vom]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VOM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1vom]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VOM FirstGlance]. <br>
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Myosin\|Myosin]]	+	*[[Myosin 3D Structures\|Myosin 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 11735]]		[[Category: Atcc 11735]]
		+	[[Category: Large Structures]]
	[[Category: Rayment, I]]		[[Category: Rayment, I]]
	[[Category: Smith, C A]]		[[Category: Smith, C A]]

OCA at 07:25, 4 April 2018

OCA — Wed, 04 Apr 2018 07:25:11 GMT

←Older revision		Revision as of 07:25, 4 April 2018
Line 1:		Line 1:
		+
	==COMPLEX BETWEEN DICTYOSTELIUM MYOSIN AND MGADP AND VANADATE AT 1.9A RESOLUTION==		==COMPLEX BETWEEN DICTYOSTELIUM MYOSIN AND MGADP AND VANADATE AT 1.9A RESOLUTION==
	<StructureSection load='1vom' size='340' side='right' caption='[[1vom]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1vom' size='340' side='right' caption='[[1vom]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1vom]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VOM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1vom]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VOM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></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=1vom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vom OCA], [http://pdbe.org/1vom PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vom RCSB], [http://www.ebi.ac.uk/pdbsum/1vom 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=1vom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vom OCA], [http://pdbe.org/1vom PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vom RCSB], [http://www.ebi.ac.uk/pdbsum/1vom PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1vom ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vo/1vom_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vo/1vom_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>
	</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=1vom ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:51, 11 September 2015

OCA — Fri, 11 Sep 2015 23:51:17 GMT

←Older revision		Revision as of 23:51, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1vom' size='340' side='right' caption='[[1vom]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1vom' size='340' side='right' caption='[[1vom]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1vom]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Dictyostelium_discoideum Dictyostelium discoideum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VOM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1vom]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VOM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></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=1vom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vom OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vom RCSB], [http://www.ebi.ac.uk/pdbsum/1vom 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=1vom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vom OCA], [http://pdbe.org/1vom PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vom RCSB], [http://www.ebi.ac.uk/pdbsum/1vom PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	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 1vom" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dictyostelium discoideum~~]]	+	[[Category: Atcc 11735]]
	[[Category: Rayment, I]]		[[Category: Rayment, I]]
	[[Category: Smith, C A]]		[[Category: Smith, C A]]

OCA at 21:03, 25 December 2014

OCA — Thu, 25 Dec 2014 21:03:01 GMT

←Older revision		Revision as of 21:03, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1vom]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VOM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1vom]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VOM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene></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=1vom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vom OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vom RCSB], [http://www.ebi.ac.uk/pdbsum/1vom 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=1vom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vom OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vom RCSB], [http://www.ebi.ac.uk/pdbsum/1vom PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MYS2_DICDI MYS2_DICDI]] Myosin is a protein that binds to actin and has ATPase activity that is activated by actin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Dictyostelium discoideum]]		[[Category: Dictyostelium discoideum]]
-	[[Category: Rayment, I.]]	+	[[Category: Rayment, I]]
-	[[Category: Smith, C A.]]	+	[[Category: Smith, C A]]
	[[Category: Molecular motor]]		[[Category: Molecular motor]]
	[[Category: Muscle protein]]		[[Category: Muscle protein]]
	[[Category: Myosin]]		[[Category: Myosin]]
	[[Category: Transition-state analog]]		[[Category: Transition-state analog]]

OCA at 22:21, 28 September 2014

OCA — Sun, 28 Sep 2014 22:21:10 GMT

←Older revision		Revision as of 22:21, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1vom.~~png\|left~~\|200px]]	+	==COMPLEX BETWEEN DICTYOSTELIUM MYOSIN AND MGADP AND VANADATE AT 1.9A RESOLUTION==
		+	<StructureSection load='1vom' size='340' side='right' caption='[[1vom]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1vom]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VOM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VO4:VANADATE+ION'>VO4</scene><br>
		+	<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=1vom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vom OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vom RCSB], [http://www.ebi.ac.uk/pdbsum/1vom 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/vo/1vom_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 structure of the vanadate-trapped ADP complex of a truncated head of Dictyostelium myosin II consisting of residues Asp 2-Asn 762 has been determined by molecular replacement at 1.9 A resolution and refined to a crystallographic R-factor of 19.4%. The crystals belong to the orthorhombic space group C2221 where a = 84.50 A, b = 145.4 A, and c = 152.8 A. The conformation of the protein is similar to that of MgADP.AlF4.SlDc [Fisher, A.J., et al. (1995) Biochemistry 34, 8960-8972]. The nucleotide binding site contains a complex between MgADP and vanadate where MgADP exhibits a very similar conformation to that seen in previous complexes. The vanadate ion adopts a trigonal bipyramidal coordination. The three equatorial oxygen ligands are fairly short, average 1.7 A, relative to a single bond distance of approximately 1.8 A and are coordinated to the magnesium ion, N zeta of Lys 185, and five other protein ligands. The apical coordination to the vanadate ion is filled by a terminal oxygen on the beta-phosphate of ADP and a water molecule at bond distances of 2.1 and 2.3 A, respectively. The long length of the apical bonds suggests that the bond order is considerably less than unity. This structure confirms the earlier suggestion that vanadate is a model for the transition state of ATP hydrolysis and thus provides insight into those factors that are responsible for catalysis. In particular, it shows that the protein ligands and water structure surrounding the gamma-phosphate pocket are oriented to stabilize a water molecule in an appropriate position for in-line nucleophilic attack on the gamma-phosphorus of ATP. This structure reveals also an orientation of the COOH-terminal region beyond Thr 688 which is very different from that observed in either MgADP.BeFx.SlDc or chicken skeletal myosin subfragment 1. This is consistent with the COOH-terminal region of the molecule playing an important role in the transduction of chemical energy of hydrolysis of ATP into mechanical movement.

-	~~{{STRUCTURE_1vom\| PDB=1vom \| SCENE= }}~~	+	X-ray structure of the magnesium(II).ADP.vanadate complex of the Dictyostelium discoideum myosin motor domain to 1.9 A resolution.,Smith CA, Rayment I Biochemistry. 1996 Apr 30;35(17):5404-17. PMID:8611530<ref>PMID:8611530</ref>

-	~~===COMPLEX BETWEEN DICTYOSTELIUM MYOSIN AND MGADP AND VANADATE AT 1.9A RESOLUTION===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8611530}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1vom]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA].~~	+

	==See Also==		==See Also==
	*[[Myosin\|Myosin]]		*[[Myosin\|Myosin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:008611530<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Dictyostelium discoideum]]		[[Category: Dictyostelium discoideum]]
	[[Category: Rayment, I.]]		[[Category: Rayment, I.]]

OCA at 21:37, 20 October 2012

OCA — Sat, 20 Oct 2012 21:37:06 GMT

←Older revision		Revision as of 21:37, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1vom]] is a 1 chain structure ~~of [[Myosin]]~~ with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA].	+	[[1vom]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VOM OCA].

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

OCA at 13:46, 27 July 2012

OCA — Fri, 27 Jul 2012 13:46:42 GMT

←Older revision		Revision as of 13:46, 27 July 2012
Line 1:		Line 1:
	[[Image:1vom.png\|left\|200px]]		[[Image:1vom.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1vom", 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_1vom\| PDB=1vom \| SCENE= }}		{{STRUCTURE_1vom\| PDB=1vom \| SCENE= }}

	===COMPLEX BETWEEN DICTYOSTELIUM MYOSIN AND MGADP AND VANADATE AT 1.9A RESOLUTION===		===COMPLEX BETWEEN DICTYOSTELIUM MYOSIN AND MGADP AND VANADATE AT 1.9A RESOLUTION===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_8611530}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 8611530 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_8611530}}		{{ABSTRACT_PUBMED_8611530}}

Line 22:		Line 11:

	==See Also==		==See Also==
-	*[[Myosin]]	+	*[[Myosin\|Myosin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~8611530~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:008611530</ref><references group="xtra"/>
	[[Category: Dictyostelium discoideum]]		[[Category: Dictyostelium discoideum]]
	[[Category: Rayment, I.]]		[[Category: Rayment, I.]]

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

OCA — Mon, 27 Dec 2010 00:01:51 GMT

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

←Older revision

Revision as of 00:01, 27 December 2010