5u35 - Revision history

OCA at 14:24, 6 March 2024

OCA — Wed, 06 Mar 2024 14:24:55 GMT

←Older revision		Revision as of 14:24, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5u35' size='340' side='right'caption='[[5u35]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5u35' size='340' side='right'caption='[[5u35]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u35]] 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=5U35 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5U35 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u35]] 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=5U35 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U35 FirstGlance]. <br>
-	</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=MXE:2-METHOXYETHANOL'>MXE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</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]] 1.8Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5u35 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u35 OCA], [~~http~~://pdbe.org/5u35 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5u35 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5u35 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5u35 ProSAT]</span></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=MXE:2-METHOXYETHANOL'>MXE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</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=5u35 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u35 OCA], [https://pdbe.org/5u35 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u35 RCSB], [https://www.ebi.ac.uk/pdbsum/5u35 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u35 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 5u35" 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: Zwart~~, P H]]~~	+	[[Category: Zwart PH]]
-	~~[[Category: De novo ntf2]]~~	+
-	~~[[Category: De novo protein~~]]	+

OCA at 12:25, 23 September 2020

OCA — Wed, 23 Sep 2020 12:25:25 GMT

←Older revision		Revision as of 12:25, 23 September 2020
Line 1:		Line 1:

	==Crystal structure of a de novo designed protein with curved beta-sheet==		==Crystal structure of a de novo designed protein with curved beta-sheet==
-	<StructureSection load='5u35' size='340' side='right' caption='[[5u35]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5u35' size='340' side='right'caption='[[5u35]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u35]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U35 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5U35 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u35]] 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=5U35 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5U35 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=MXE:2-METHOXYETHANOL'>MXE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</scene></td></tr>	+	</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=MXE:2-METHOXYETHANOL'>MXE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</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=5u35 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u35 OCA], [http://pdbe.org/5u35 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u35 RCSB], [http://www.ebi.ac.uk/pdbsum/5u35 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u35 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5u35 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u35 OCA], [http://pdbe.org/5u35 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u35 RCSB], [http://www.ebi.ac.uk/pdbsum/5u35 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u35 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Synthetic construct sequences]]
	[[Category: Baker, D]]		[[Category: Baker, D]]
	[[Category: Basanta, B]]		[[Category: Basanta, B]]

OCA at 11:18, 1 February 2017

OCA — Wed, 01 Feb 2017 11:18:09 GMT

←Older revision		Revision as of 11:18, 1 February 2017
Line 7:		Line 7:
	<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=5u35 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u35 OCA], [http://pdbe.org/5u35 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u35 RCSB], [http://www.ebi.ac.uk/pdbsum/5u35 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u35 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=5u35 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u35 OCA], [http://pdbe.org/5u35 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u35 RCSB], [http://www.ebi.ac.uk/pdbsum/5u35 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u35 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 5u35" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 23:47, 25 January 2017

OCA — Wed, 25 Jan 2017 23:47:46 GMT

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

-	~~The entry~~ 5u35 ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of a de novo designed protein with curved beta-sheet==
-		+	<StructureSection load='5u35' size='340' side='right' caption='[[5u35]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors~~: ~~Oberdorfer, G~~., ~~Marcos~~, E., ~~Basanta~~, B., ~~Chidyausiku, T~~.M., ~~Sankaran~~, B., ~~Zwart, P~~.H., Baker, D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5u35]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U35 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U35 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of a de novo designed protein 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=MXE:2-METHOXYETHANOL'>MXE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PG6:1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE'>PG6</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5u35 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u35 OCA], [http://pdbe.org/5u35 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u35 RCSB], [http://www.ebi.ac.uk/pdbsum/5u35 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u35 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: Zwart, P H]]
-	[[Category: ~~Baker, D~~]]	+	[[Category: De novo ntf2]]
-	[[Category: ~~Chidyausiku, T.M]]~~	+	[[Category: De novo protein]]
-	~~[[Category: Marcos, E]]~~	+
-	~~[[Category: Zwart, P.H~~]]	+

OCA at 20:20, 22 December 2016

OCA — Thu, 22 Dec 2016 20:20:32 GMT

←Older revision		Revision as of 20:20, 22 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5u35 is ON HOLD	+	The entry 5u35 is ON HOLD until Paper Publication

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

OCA at 17:36, 15 December 2016

OCA — Thu, 15 Dec 2016 17:36:16 GMT

←Older revision		Revision as of 17:36, 15 December 2016
Line 3:		Line 3:
	The entry 5u35 is ON HOLD		The entry 5u35 is ON HOLD

-	Authors: Oberdorfer, G., Marcos, E., Basanta, B., Chidyausiku, T.M., Sankaran, B., Zwart, P. H., Baker, D.	+	Authors: Oberdorfer, G., Marcos, E., Basanta, B., Chidyausiku, T.M., Sankaran, B., Zwart, P.H., Baker, D.

	Description: Crystal structure of a de novo designed protein with curved beta-sheet		Description: Crystal structure of a de novo designed protein with curved beta-sheet
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Oberdorfer, G]]		[[Category: Oberdorfer, G]]
-	[[Category: Zwart, P. H]]
	[[Category: Sankaran, B]]		[[Category: Sankaran, B]]
	[[Category: Basanta, B]]		[[Category: Basanta, B]]
Line 14:		Line 13:
	[[Category: Chidyausiku, T.M]]		[[Category: Chidyausiku, T.M]]
	[[Category: Marcos, E]]		[[Category: Marcos, E]]
		+	[[Category: Zwart, P.H]]

OCA: Protected "5u35" [edit=sysop:move=sysop]

OCA — Fri, 09 Dec 2016 18:15:15 GMT

Protected "5u35" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:15, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5u35 is ON HOLD Authors: Oberdorfer, G., Marcos, E., Basanta, B., Chidyausiku, T.M., Sankaran, B., Zwart, P. H., Baker, D. Description: Crystal str...

OCA — Fri, 09 Dec 2016 18:15:14 GMT

New page: '''Unreleased structure''' The entry 5u35 is ON HOLD Authors: Oberdorfer, G., Marcos, E., Basanta, B., Chidyausiku, T.M., Sankaran, B., Zwart, P. H., Baker, D. Description: Crystal str...

New page

'''Unreleased structure'''

The entry 5u35 is ON HOLD

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

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