6n9h - Revision history

OCA at 14:47, 13 March 2024

OCA — Wed, 13 Mar 2024 14:47:04 GMT

←Older revision		Revision as of 14:47, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6n9h' size='340' side='right'caption='[[6n9h]], [[Resolution\|resolution]] 1.04Å' scene=''>		<StructureSection load='6n9h' size='340' side='right'caption='[[6n9h]], [[Resolution\|resolution]] 1.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n9h]] is a 1 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=6N9H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N9H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n9h]] is a 1 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=6N9H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N9H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=308:(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DECAN-1-AMINE'>308</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.039Å</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=6n9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9h OCA], [~~http~~://pdbe.org/6n9h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n9h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n9h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9h ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=308:(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DECAN-1-AMINE'>308</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6n9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9h OCA], [https://pdbe.org/6n9h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n9h RCSB], [https://www.ebi.ac.uk/pdbsum/6n9h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9h ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The computational design of a symmetric protein homo-oligomer that binds a symmetry-matched small molecule larger than a metal ion has not yet been achieved. We used de novo protein design to create a homo-trimeric protein that binds the C3 symmetric small molecule drug amantadine with each protein monomer making identical interactions with each face of the small molecule. Solution NMR data show that the protein has regular three-fold symmetry and undergoes localized structural changes upon ligand binding. A high-resolution X-ray structure reveals a close overall match to the design model with the exception of water molecules in the amantadine binding site not included in the Rosetta design calculations, and a neutron structure provides experimental validation of the computationally designed hydrogen-bond networks. Exploration of approaches to generate a small molecule inducible homo-trimerization system based on the design highlight challenges that must be overcome to computationally design such systems.
-
-	De novo design of a homo-trimeric amantadine-binding protein.,Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DA, Baker D Elife. 2019 Dec 19;8. pii: 47839. doi: 10.7554/eLife.47839. PMID:31854299<ref>PMID:31854299</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6n9h" 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: Park, J]]	+	[[Category: Park J]]
-	~~[[Category: Amantadine-binding protein]]~~	+
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Helical bundle]]~~	+
-	~~[[Category: Trimer~~]]	+

OCA at 11:38, 1 January 2020

OCA — Wed, 01 Jan 2020 11:38:09 GMT

←Older revision		Revision as of 11:38, 1 January 2020
Line 3:		Line 3:
	<StructureSection load='6n9h' size='340' side='right'caption='[[6n9h]], [[Resolution\|resolution]] 1.04Å' scene=''>		<StructureSection load='6n9h' size='340' side='right'caption='[[6n9h]], [[Resolution\|resolution]] 1.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n9h]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N9H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n9h]] is a 1 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=6N9H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N9H FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=308:(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DECAN-1-AMINE'>308</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=308:(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DECAN-1-AMINE'>308</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6n9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9h OCA], [http://pdbe.org/6n9h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n9h RCSB], [http://www.ebi.ac.uk/pdbsum/6n9h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9h 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=6n9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9h OCA], [http://pdbe.org/6n9h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n9h RCSB], [http://www.ebi.ac.uk/pdbsum/6n9h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9h ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The computational design of a symmetric protein homo-oligomer that binds a symmetry-matched small molecule larger than a metal ion has not yet been achieved. We used de novo protein design to create a homo-trimeric protein that binds the C3 symmetric small molecule drug amantadine with each protein monomer making identical interactions with each face of the small molecule. Solution NMR data show that the protein has regular three-fold symmetry and undergoes localized structural changes upon ligand binding. A high-resolution X-ray structure reveals a close overall match to the design model with the exception of water molecules in the amantadine binding site not included in the Rosetta design calculations, and a neutron structure provides experimental validation of the computationally designed hydrogen-bond networks. Exploration of approaches to generate a small molecule inducible homo-trimerization system based on the design highlight challenges that must be overcome to computationally design such systems.
		+
		+	De novo design of a homo-trimeric amantadine-binding protein.,Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DA, Baker D Elife. 2019 Dec 19;8. pii: 47839. doi: 10.7554/eLife.47839. PMID:31854299<ref>PMID:31854299</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6n9h" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Synthetic construct sequences]]
	[[Category: Baker, D]]		[[Category: Baker, D]]
	[[Category: Park, J]]		[[Category: Park, J]]

OCA at 07:43, 18 December 2019

OCA — Wed, 18 Dec 2019 07:43:11 GMT

←Older revision		Revision as of 07:43, 18 December 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6n9h ~~is ON HOLD until Paper Publication~~	+	==De novo designed homo-trimeric amantadine-binding protein==
-		+	<StructureSection load='6n9h' size='340' side='right'caption='[[6n9h]], [[Resolution\|resolution]] 1.04Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6n9h]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N9H FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=308:(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DECAN-1-AMINE'>308</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6n9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9h OCA], [http://pdbe.org/6n9h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n9h RCSB], [http://www.ebi.ac.uk/pdbsum/6n9h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9h ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Baker, D]]
		+	[[Category: Park, J]]
		+	[[Category: Amantadine-binding protein]]
		+	[[Category: De novo protein]]
		+	[[Category: Helical bundle]]
		+	[[Category: Trimer]]

OCA: Protected "6n9h" [edit=sysop:move=sysop]

OCA — Wed, 12 Dec 2018 05:22:52 GMT

Protected "6n9h" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:22, 12 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n9h is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 12 Dec 2018 05:22:51 GMT

New page: '''Unreleased structure''' The entry 6n9h is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6n9h is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]