5tph - Revision history

OCA at 14:22, 6 March 2024

2024-03-06T14:22:45Z

←Older revision		Revision as of 14:22, 6 March 2024
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	<StructureSection load='5tph' size='340' side='right'caption='[[5tph]], [[Resolution\|resolution]] 2.47Å' scene=''>		<StructureSection load='5tph' size='340' side='right'caption='[[5tph]], [[Resolution\|resolution]] 2.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tph]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TPH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tph]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TPH FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CL:CHLORIDE+ION'>CL</scene~~>, ~~<scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.47Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5tpj\|5tpj]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5tph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tph OCA], [~~http~~://pdbe.org/5tph PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tph RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tph PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tph 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=5tph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tph OCA], [https://pdbe.org/5tph PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tph RCSB], [https://www.ebi.ac.uk/pdbsum/5tph PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tph ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Active sites and ligand-binding cavities in native proteins are often formed by curved beta sheets, and the ability to control beta-sheet curvature would allow design of binding proteins with cavities customized to specific ligands. Toward this end, we investigated the mechanisms controlling beta-sheet curvature by studying the geometry of beta sheets in naturally occurring protein structures and folding simulations. The principles emerging from this analysis were used to design, de novo, a series of proteins with curved beta sheets topped with alpha helices. Nuclear magnetic resonance and crystal structures of the designs closely match the computational models, showing that beta-sheet curvature can be controlled with atomic-level accuracy. Our approach enables the design of proteins with cavities and provides a route to custom design ligand-binding and catalytic sites.
-
-	Principles for designing proteins with cavities formed by curved beta sheets.,Marcos E, Basanta B, Chidyausiku TM, Tang Y, Oberdorfer G, Liu G, Swapna GV, Guan R, Silva DA, Dou J, Pereira JH, Xiao R, Sankaran B, Zwart PH, Montelione GT, Baker D Science. 2017 Jan 13;355(6321):201-206. doi: 10.1126/science.aah7389. PMID:28082595<ref>PMID:28082595</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5tph" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Baker, D]]	+	[[Category: Baker D]]
-	[[Category: Basanta, B]]	+	[[Category: Basanta B]]
-	[[Category: Chidyausiku~~, T M~~]]	+	[[Category: Chidyausiku TM]]
-	[[Category: Marcos, E]]	+	[[Category: Marcos E]]
-	[[Category: Oberdorfer, G]]	+	[[Category: Oberdorfer G]]
-	[[Category: Sankaran, B]]	+	[[Category: Sankaran B]]
-	~~[[Category: De novo ntf2]]~~	+
-	~~[[Category: De novo protein~~]]	+

OCA at 09:25, 4 December 2019

2019-12-04T09:25:22Z

←Older revision		Revision as of 09:25, 4 December 2019
Line 1:		Line 1:

	==Crystal structure of a de novo designed protein homodimer with curved beta-sheet==		==Crystal structure of a de novo designed protein homodimer with curved beta-sheet==
-	<StructureSection load='5tph' size='340' side='right' caption='[[5tph]], [[Resolution\|resolution]] 2.47Å' scene=''>	+	<StructureSection load='5tph' size='340' side='right'caption='[[5tph]], [[Resolution\|resolution]] 2.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tph]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPH FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tph]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPH FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Synthetic construct sequences]]		[[Category: Synthetic construct sequences]]
	[[Category: Baker, D]]		[[Category: Baker, D]]

OCA at 19:14, 15 November 2017

2017-11-15T19:14:31Z

←Older revision		Revision as of 19:14, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5tph' size='340' side='right' caption='[[5tph]], [[Resolution\|resolution]] 2.47Å' scene=''>		<StructureSection load='5tph' size='340' side='right' caption='[[5tph]], [[Resolution\|resolution]] 2.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tph]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tph]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPH FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tpj\|5tpj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tpj\|5tpj]]</td></tr>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Synthetic construct sequences]]
	[[Category: Baker, D]]		[[Category: Baker, D]]
	[[Category: Basanta, B]]		[[Category: Basanta, B]]

OCA at 11:13, 1 February 2017

2017-02-01T11:13:45Z

←Older revision		Revision as of 11:13, 1 February 2017
Line 8:		Line 8:
	<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=5tph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tph OCA], [http://pdbe.org/5tph PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tph RCSB], [http://www.ebi.ac.uk/pdbsum/5tph PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tph 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=5tph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tph OCA], [http://pdbe.org/5tph PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tph RCSB], [http://www.ebi.ac.uk/pdbsum/5tph PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tph ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Active sites and ligand-binding cavities in native proteins are often formed by curved beta sheets, and the ability to control beta-sheet curvature would allow design of binding proteins with cavities customized to specific ligands. Toward this end, we investigated the mechanisms controlling beta-sheet curvature by studying the geometry of beta sheets in naturally occurring protein structures and folding simulations. The principles emerging from this analysis were used to design, de novo, a series of proteins with curved beta sheets topped with alpha helices. Nuclear magnetic resonance and crystal structures of the designs closely match the computational models, showing that beta-sheet curvature can be controlled with atomic-level accuracy. Our approach enables the design of proteins with cavities and provides a route to custom design ligand-binding and catalytic sites.
		+
		+	Principles for designing proteins with cavities formed by curved beta sheets.,Marcos E, Basanta B, Chidyausiku TM, Tang Y, Oberdorfer G, Liu G, Swapna GV, Guan R, Silva DA, Dou J, Pereira JH, Xiao R, Sankaran B, Zwart PH, Montelione GT, Baker D Science. 2017 Jan 13;355(6321):201-206. doi: 10.1126/science.aah7389. PMID:28082595<ref>PMID:28082595</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5tph" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 23:47, 25 January 2017

2017-01-25T23:47:06Z

←Older revision		Revision as of 23:47, 25 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tph ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of a de novo designed protein homodimer with curved beta-sheet==
-		+	<StructureSection load='5tph' size='340' side='right' caption='[[5tph]], [[Resolution\|resolution]] 2.47Å' scene=''>
-	~~Authors~~: ~~Basanta~~, B., ~~Marcos, E~~., ~~Oberdorfer, G~~., ~~Chidyausiku, T~~.M., ~~Sankaran, B~~., Baker, D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5tph]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPH FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of a de novo designed protein homodimer with curved beta-sheet~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tpj\|5tpj]]</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=5tph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tph OCA], [http://pdbe.org/5tph PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tph RCSB], [http://www.ebi.ac.uk/pdbsum/5tph PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tph ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Baker, D]]
		+	[[Category: Basanta, B]]
		+	[[Category: Chidyausiku, T M]]
		+	[[Category: Marcos, E]]
	[[Category: Oberdorfer, G]]		[[Category: Oberdorfer, G]]
	[[Category: Sankaran, B]]		[[Category: Sankaran, B]]
-	[[Category: ~~Basanta, B~~]]	+	[[Category: De novo ntf2]]
-	[[Category: ~~Baker, D]]~~	+	[[Category: De novo protein]]
-	~~[[Category: Chidyausiku, T.M]]~~	+
-	~~[[Category: Marcos, E~~]]	+

OCA at 17:00, 2 November 2016

2016-11-02T17:00:10Z

←Older revision		Revision as of 17:00, 2 November 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Basanta, B., Marcos, E., Oberdorfer, G., Chidyausiku, T.M., Sankaran, B., Baker, D.		Authors: Basanta, B., Marcos, E., Oberdorfer, G., Chidyausiku, T.M., Sankaran, B., Baker, D.

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

2016-10-26T17:21:25Z

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

←Older revision

Revision as of 17:21, 26 October 2016

OCA: New page: '''Unreleased structure''' The entry 5tph is ON HOLD Authors: Basanta, B., Marcos, E., Oberdorfer, G., Chidyausiku, T.M., Sankaran, B., Baker, D. Description: Crystal structure of a de...

2016-10-26T17:21:23Z

New page: '''Unreleased structure''' The entry 5tph is ON HOLD Authors: Basanta, B., Marcos, E., Oberdorfer, G., Chidyausiku, T.M., Sankaran, B., Baker, D. Description: Crystal structure of a de...

New page

'''Unreleased structure'''

The entry 5tph is ON HOLD

Authors: Basanta, B., Marcos, E., Oberdorfer, G., Chidyausiku, T.M., Sankaran, B., Baker, D.

Description: Crystal structure of a de novo designed protein homodimer with curved beta-sheet
[[Category: Unreleased Structures]]
[[Category: Oberdorfer, G]]
[[Category: Sankaran, B]]
[[Category: Basanta, B]]
[[Category: Baker, D]]
[[Category: Chidyausiku, T.M]]
[[Category: Marcos, E]]