6naf - Revision history

OCA at 09:15, 25 October 2023

OCA — Wed, 25 Oct 2023 09:15:30 GMT

←Older revision		Revision as of 09:15, 25 October 2023
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	<StructureSection load='6naf' size='340' side='right'caption='[[6naf]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='6naf' size='340' side='right'caption='[[6naf]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6naf]] 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=6NAF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NAF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6naf]] 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=6NAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NAF 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=DOD:DEUTERATED+WATER'>DOD</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">Hybrid , Neutron Diffraction , X-ray diffraction, [[Resolution\|Resolution]] 1.923Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6n9h\|6n9h]]~~</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=DOD:DEUTERATED+WATER'>DOD</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=6naf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6naf OCA], [~~http~~://pdbe.org/6naf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6naf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6naf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6naf 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=6naf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6naf OCA], [https://pdbe.org/6naf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6naf RCSB], [https://www.ebi.ac.uk/pdbsum/6naf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6naf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Synthetic construct ~~sequences~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Baker, D]]	+	[[Category: Baker D]]
-	[[Category: Cuneo~~, M J~~]]	+	[[Category: Cuneo MJ]]
-	[[Category: Myles~~, D A.A~~]]	+	[[Category: Myles DAA]]
-	[[Category: Park, J]]	+	[[Category: Park J]]
-	[[Category: Selvaraj, B]]	+	[[Category: Selvaraj B]]
-	~~[[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 11:38:27 GMT

←Older revision		Revision as of 11:38, 1 January 2020
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	<StructureSection load='6naf' size='340' side='right'caption='[[6naf]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='6naf' size='340' side='right'caption='[[6naf]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6naf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NAF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NAF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6naf]] 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=6NAF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NAF 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=DOD:DEUTERATED+WATER'>DOD</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=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6n9h\|6n9h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6n9h\|6n9h]]</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=6naf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6naf OCA], [http://pdbe.org/6naf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6naf RCSB], [http://www.ebi.ac.uk/pdbsum/6naf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6naf 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=6naf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6naf OCA], [http://pdbe.org/6naf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6naf RCSB], [http://www.ebi.ac.uk/pdbsum/6naf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6naf 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 6naf" 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: Cuneo, M J]]		[[Category: Cuneo, M J]]

OCA at 07:43, 18 December 2019

OCA — Wed, 18 Dec 2019 07:43:14 GMT

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

-	~~The entry~~ 6naf ~~is ON HOLD until Paper Publication~~	+	==De novo designed homo-trimeric amantadine-binding protein==
-		+	<StructureSection load='6naf' size='340' side='right'caption='[[6naf]], [[Resolution\|resolution]] 1.92Å' scene=''>
-	~~Authors~~: ~~Selvaraj, B~~., ~~Park~~, J., ~~Cuneo~~, M.J., ~~Myles~~, D.A.A., ~~Baker~~, D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6naf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NAF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NAF FirstGlance]. <br>
-	~~Description: De novo designed homo-trimeric amantadine-binding protein~~	+	</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=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6n9h\|6n9h]]</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=6naf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6naf OCA], [http://pdbe.org/6naf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6naf RCSB], [http://www.ebi.ac.uk/pdbsum/6naf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6naf ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Baker, D]]		[[Category: Baker, D]]
-	[[Category: Cuneo, M.J]]	+	[[Category: Cuneo, M J]]
		+	[[Category: Myles, D A.A]]
		+	[[Category: Park, J]]
	[[Category: Selvaraj, B]]		[[Category: Selvaraj, B]]
-	[[Category: ~~Park, J~~]]	+	[[Category: Amantadine-binding protein]]
-	[[Category: ~~Myles, D.A.A~~]]	+	[[Category: De novo protein]]
		+	[[Category: Helical bundle]]
		+	[[Category: Trimer]]

OCA at 06:33, 19 December 2018

OCA — Wed, 19 Dec 2018 06:33:23 GMT

←Older revision		Revision as of 06:33, 19 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6naf is ON HOLD	+	The entry 6naf is ON HOLD until Paper Publication

	Authors: Selvaraj, B., Park, J., Cuneo, M.J., Myles, D.A.A., Baker, D.		Authors: Selvaraj, B., Park, J., Cuneo, M.J., Myles, D.A.A., Baker, D.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Baker, D]]		[[Category: Baker, D]]
-	[[Category: Park, J]]
	[[Category: Cuneo, M.J]]		[[Category: Cuneo, M.J]]
-	[[Category: Myles, D.A.A]]
	[[Category: Selvaraj, B]]		[[Category: Selvaraj, B]]
		+	[[Category: Park, J]]
		+	[[Category: Myles, D.A.A]]

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

OCA — Wed, 12 Dec 2018 05:25:10 GMT

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

←Older revision

Revision as of 05:25, 12 December 2018

OCA: New page: '''Unreleased structure''' The entry 6naf is ON HOLD Authors: Selvaraj, B., Park, J., Cuneo, M.J., Myles, D.A.A., Baker, D. Description: De novo designed homo-trimeric amantadine-bindi...

OCA — Wed, 12 Dec 2018 05:25:08 GMT

New page: '''Unreleased structure''' The entry 6naf is ON HOLD Authors: Selvaraj, B., Park, J., Cuneo, M.J., Myles, D.A.A., Baker, D. Description: De novo designed homo-trimeric amantadine-bindi...

New page

'''Unreleased structure'''

The entry 6naf is ON HOLD

Authors: Selvaraj, B., Park, J., Cuneo, M.J., Myles, D.A.A., Baker, D.

Description: De novo designed homo-trimeric amantadine-binding protein
[[Category: Unreleased Structures]]
[[Category: Baker, D]]
[[Category: Park, J]]
[[Category: Cuneo, M.J]]
[[Category: Myles, D.A.A]]
[[Category: Selvaraj, B]]