5amk - Revision history

OCA at 11:13, 10 January 2024

2024-01-10T11:13:28Z

←Older revision		Revision as of 11:13, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5amk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Magnetospirillum_gryphiswaldense_MSR-1 Magnetospirillum gryphiswaldense MSR-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AMK FirstGlance]. <br>		<table><tr><td colspan='2'>[[5amk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Magnetospirillum_gryphiswaldense_MSR-1 Magnetospirillum gryphiswaldense MSR-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AMK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</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]] 2.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5amk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amk OCA], [https://pdbe.org/5amk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5amk RCSB], [https://www.ebi.ac.uk/pdbsum/5amk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5amk 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=5amk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amk OCA], [https://pdbe.org/5amk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5amk RCSB], [https://www.ebi.ac.uk/pdbsum/5amk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5amk ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:15, 31 May 2023

2023-05-31T06:15:07Z

←Older revision		Revision as of 06:15, 31 May 2023
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	<StructureSection load='5amk' size='340' side='right'caption='[[5amk]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='5amk' size='340' side='right'caption='[[5amk]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5amk]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Maggm Maggm~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5AMK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5amk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Magnetospirillum_gryphiswaldense_MSR-1 Magnetospirillum gryphiswaldense MSR-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AMK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</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">[[5amh\|5amh]], [[5ami\|5ami]], [[5amj\|5amj]]~~</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=5amk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amk OCA], [https://pdbe.org/5amk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5amk RCSB], [https://www.ebi.ac.uk/pdbsum/5amk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5amk ProSAT]</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=5amk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amk OCA], [~~http~~://pdbe.org/5amk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5amk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5amk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5amk ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A4TVL0_9PROT A4TVL0_9PROT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Ubiquitin protein ligase\|Ubiquitin protein ligase]]	+	*[[Ubiquitin protein ligase 3D structures\|Ubiquitin protein ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Maggm~~]]	+	[[Category: Magnetospirillum gryphiswaldense MSR-1]]
-	[[Category: ~~Alvarez, B Hernandez~~]]	+	[[Category: Hartmann MD]]
-	[[Category: ~~Hartmann, M D~~]]	+	[[Category: Hernandez Alvarez B]]
-	[[Category: Lupas~~, A N]]~~	+	[[Category: Lupas AN]]
-	~~[[Category: Aromatic cage]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Teratogenicity~~]]	+

OCA at 07:34, 3 July 2019

2019-07-03T07:34:19Z

←Older revision		Revision as of 07:34, 3 July 2019
Line 1:		Line 1:

	==Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form==		==Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form==
-	<StructureSection load='5amk' size='340' side='right' caption='[[5amk]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='5amk' size='340' side='right'caption='[[5amk]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5amk]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AMK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5amk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Maggm Maggm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AMK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</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"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</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">[[5amh\|5amh]], [[5ami\|5ami]], [[5amj\|5amj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5amh\|5amh]], [[5ami\|5ami]], [[5amj\|5amj]]</td></tr>
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Maggm]]
	[[Category: Alvarez, B Hernandez]]		[[Category: Alvarez, B Hernandez]]
	[[Category: Hartmann, M D]]		[[Category: Hartmann, M D]]

OCA at 13:46, 5 April 2017

2017-04-05T13:46:38Z

←Older revision		Revision as of 13:46, 5 April 2017
Line 1:		Line 1:
		+
	==Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form==		==Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form==
	<StructureSection load='5amk' size='340' side='right' caption='[[5amk]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='5amk' size='340' side='right' caption='[[5amk]], [[Resolution\|resolution]] 2.90Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</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"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</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">[[5amh\|5amh]], [[5ami\|5ami]], [[5amj\|5amj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5amh\|5amh]], [[5ami\|5ami]], [[5amj\|5amj]]</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=5amk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5amk RCSB], [http://www.ebi.ac.uk/pdbsum/5amk 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=5amk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amk OCA], [http://pdbe.org/5amk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5amk RCSB], [http://www.ebi.ac.uk/pdbsum/5amk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5amk ProSAT]</span></td></tr>
	</table>		</table>
	<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 5amk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ubiquitin protein ligase\|Ubiquitin protein ligase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:03, 1 July 2015

2015-07-01T12:03:33Z

←Older revision		Revision as of 12:03, 1 July 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form==
		+	<StructureSection load='5amk' size='340' side='right' caption='[[5amk]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5amk]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AMK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</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">[[5amh\|5amh]], [[5ami\|5ami]], [[5amj\|5amj]]</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=5amk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5amk RCSB], [http://www.ebi.ac.uk/pdbsum/5amk PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cereblon, a primary target of thalidomide and its derivatives, has been characterized structurally from both bacteria and animals. Especially well studied is the thalidomide binding domain, CULT, which shows an invariable structure across different organisms and in complex with different ligands. Here, based on a series of crystal structures of a bacterial representative, we reveal the conformational flexibility and structural dynamics of this domain. In particular, we follow the unfolding of large fractions of the domain upon release of thalidomide in the crystalline state. Our results imply that a third of the domain, including the thalidomide binding pocket, only folds upon ligand binding. We further characterize the structural effect of the C-terminal truncation resulting from the mental-retardation linked R419X nonsense mutation in vitro and offer a mechanistic hypothesis for its irresponsiveness to thalidomide. At 1.2A resolution, our data provide a view of thalidomide binding at atomic resolution.

-	~~The entry 5amk is ON HOLD until Paper Publication~~	+	Structural dynamics of the cereblon ligand binding domain.,Hartmann MD, Boichenko I, Coles M, Lupas AN, Hernandez Alvarez B PLoS One. 2015 May 29;10(5):e0128342. doi: 10.1371/journal.pone.0128342., eCollection 2015. PMID:26024445<ref>PMID:26024445</ref>

-	~~Authors: Hartmann~~, M.D.~~, Lupas, A.N., Hernandez Alvarez, B~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
-	[[Category: Hartmann, M.D]]	+	__TOC__
-	[[Category: Lupas, A.N]]	+	</StructureSection>
-	[[Category: ~~Hernandez Alvarez, B~~]]	+	[[Category: Alvarez, B Hernandez]]
		+	[[Category: Hartmann, M D]]
		+	[[Category: Lupas, A N]]
		+	[[Category: Aromatic cage]]
		+	[[Category: Signaling protein]]
		+	[[Category: Teratogenicity]]

OCA at 13:08, 26 March 2015

2015-03-26T13:08:23Z

←Older revision		Revision as of 13:08, 26 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5amk is ON HOLD	+	The entry 5amk is ON HOLD until Paper Publication

	Authors: Hartmann, M.D., Lupas, A.N., Hernandez Alvarez, B.		Authors: Hartmann, M.D., Lupas, A.N., Hernandez Alvarez, B.

OCA: Protected "5amk" [edit=sysop:move=sysop]

2015-03-18T11:15:06Z

Protected "5amk" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:15, 18 March 2015

OCA: New page: '''Unreleased structure''' The entry 5amk is ON HOLD Authors: Hartmann, M.D., Lupas, A.N., Hernandez Alvarez, B. Description: Cereblon isoform 4 from Magnetospirillum gryphiswaldense i...

2015-03-18T11:15:04Z

New page: '''Unreleased structure''' The entry 5amk is ON HOLD Authors: Hartmann, M.D., Lupas, A.N., Hernandez Alvarez, B. Description: Cereblon isoform 4 from Magnetospirillum gryphiswaldense i...

New page

'''Unreleased structure'''

The entry 5amk is ON HOLD

Authors: Hartmann, M.D., Lupas, A.N., Hernandez Alvarez, B.

Description: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in multiple conformations, hexagonal crystal form
[[Category: Unreleased Structures]]
[[Category: Hartmann, M.D]]
[[Category: Lupas, A.N]]
[[Category: Hernandez Alvarez, B]]