7rmy - Revision history

OCA at 07:20, 3 April 2024

2024-04-03T07:20:10Z

← Older revision		Revision as of 07:20, 3 April 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7rmy]] 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=7RMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RMY FirstGlance]. <br>		<table><tr><td colspan='2'>[[7rmy]] 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=7RMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RMY FirstGlance]. <br>
	</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=7rmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rmy OCA], [https://pdbe.org/7rmy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rmy RCSB], [https://www.ebi.ac.uk/pdbsum/7rmy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rmy ProSAT]</span></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]] 3.17Å</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=7rmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rmy OCA], [https://pdbe.org/7rmy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rmy RCSB], [https://www.ebi.ac.uk/pdbsum/7rmy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rmy ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Function follows form in biology, and the binding of small molecules requires proteins with pockets that match the shape of the ligand. For design of binding to symmetric ligands, protein homo-oligomers with matching symmetry are advantageous as each protein subunit can make identical interactions with the ligand. Here, we describe a general approach to designing hyperstable C2 symmetric proteins with pockets of diverse size and shape. We first designed repeat proteins that sample a continuum of curvatures but have low helical rise, then docked these into C2 symmetric homodimers to generate an extensive range of C2 symmetric cavities. We used this approach to design thousands of C2 symmetric homodimers, and characterized 101 of them experimentally. Of these, the geometry of 31 were confirmed by small angle X-ray scattering and 2 were shown by crystallographic analyses to be in close agreement with the computational design models. These scaffolds provide a rich set of starting points for binding a wide range of C2 symmetric compounds.

	De novo design of protein homodimers containing tunable symmetric protein pockets.,Hicks DR, Kennedy MA, Thompson KA, DeWitt M, Coventry B, Kang A, Bera AK, Brunette TJ, Sankaran B, Stoddard B, Baker D Proc Natl Acad Sci U S A. 2022 Jul 26;119(30):e2113400119. doi:, 10.1073/pnas.2113400119. Epub 2022 Jul 21. PMID:35862457<ref>PMID:35862457</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 7rmy" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 03:13, 8 September 2022

2022-09-08T03:13:59Z

← Older revision		Revision as of 03:13, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7rmy' size='340' side='right'caption='[[7rmy]], [[Resolution\|resolution]] 3.17Å' scene=''>		<StructureSection load='7rmy' size='340' side='right'caption='[[7rmy]], [[Resolution\|resolution]] 3.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7rmy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RMY FirstGlance]. <br>		<table><tr><td colspan='2'>[[7rmy]] 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=7RMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RMY FirstGlance]. <br>
	</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=7rmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rmy OCA], [https://pdbe.org/7rmy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rmy RCSB], [https://www.ebi.ac.uk/pdbsum/7rmy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rmy ProSAT]</span></td></tr>		</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=7rmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rmy OCA], [https://pdbe.org/7rmy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rmy RCSB], [https://www.ebi.ac.uk/pdbsum/7rmy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rmy ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Baker, D]]		[[Category: Synthetic construct]]
	[[Category: Bera~~, A K~~]]		[[Category: Baker D]]
	[[Category: Hicks~~, D R~~]]		[[Category: Bera AK]]
	[[Category: Kang, A]]		[[Category: Hicks DR]]
	[[Category: Sankaran, B]]		[[Category: Kang A]]
	~~[[Category: De novo design]]~~		[[Category: Sankaran B]]
	~~[[Category: De novo protein]]~~
	~~[[Category: Homodimer]]~~
	~~[[Category: Repeat protein]]~~
	~~[[Category: Tunable pocket~~]]

OCA at 05:11, 10 August 2022

2022-08-10T05:11:31Z

← Older revision		Revision as of 05:11, 10 August 2022
Line 1:		Line 1:

	==De Novo designed tunable protein pockets, D_3-337==		==De Novo designed tunable protein pockets, D_3-337==
	<StructureSection load='7rmy' size='340' side='right'caption='[[7rmy]]' scene=''>		<StructureSection load='7rmy' size='340' side='right'caption='[[7rmy]], [[Resolution\|resolution]] 3.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RMY FirstGlance]. <br>		<table><tr><td colspan='2'>[[7rmy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RMY FirstGlance]. <br>
	</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=7rmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rmy OCA], [https://pdbe.org/7rmy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rmy RCSB], [https://www.ebi.ac.uk/pdbsum/7rmy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rmy ProSAT]</span></td></tr>		</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=7rmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rmy OCA], [https://pdbe.org/7rmy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rmy RCSB], [https://www.ebi.ac.uk/pdbsum/7rmy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rmy ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Function follows form in biology, and the binding of small molecules requires proteins with pockets that match the shape of the ligand. For design of binding to symmetric ligands, protein homo-oligomers with matching symmetry are advantageous as each protein subunit can make identical interactions with the ligand. Here, we describe a general approach to designing hyperstable C2 symmetric proteins with pockets of diverse size and shape. We first designed repeat proteins that sample a continuum of curvatures but have low helical rise, then docked these into C2 symmetric homodimers to generate an extensive range of C2 symmetric cavities. We used this approach to design thousands of C2 symmetric homodimers, and characterized 101 of them experimentally. Of these, the geometry of 31 were confirmed by small angle X-ray scattering and 2 were shown by crystallographic analyses to be in close agreement with the computational design models. These scaffolds provide a rich set of starting points for binding a wide range of C2 symmetric compounds.

			De novo design of protein homodimers containing tunable symmetric protein pockets.,Hicks DR, Kennedy MA, Thompson KA, DeWitt M, Coventry B, Kang A, Bera AK, Brunette TJ, Sankaran B, Stoddard B, Baker D Proc Natl Acad Sci U S A. 2022 Jul 26;119(30):e2113400119. doi:, 10.1073/pnas.2113400119. Epub 2022 Jul 21. PMID:35862457<ref>PMID:35862457</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7rmy" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Baker D]]		[[Category: Baker, D]]
	[[Category: Bera AK]]		[[Category: Bera, A K]]
	[[Category: Hicks DR]]		[[Category: Hicks, D R]]
	[[Category: Kang A]]		[[Category: Kang, A]]
	[[Category: Sankaran B]]		[[Category: Sankaran, B]]
			[[Category: De novo design]]
			[[Category: De novo protein]]
			[[Category: Homodimer]]
			[[Category: Repeat protein]]
			[[Category: Tunable pocket]]

OCA at 04:52, 3 August 2022

2022-08-03T04:52:28Z

← Older revision		Revision as of 04:52, 3 August 2022
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7rmy is ~~ON HOLD until Paper Publication~~		==De Novo designed tunable protein pockets, D_3-337==
			<StructureSection load='7rmy' size='340' side='right'caption='[[7rmy]]' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RMY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RMY FirstGlance]. <br>
	~~Description~~:		</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=7rmy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rmy OCA], [https://pdbe.org/7rmy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rmy RCSB], [https://www.ebi.ac.uk/pdbsum/7rmy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rmy ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Baker D]]
			[[Category: Bera AK]]
			[[Category: Hicks DR]]
			[[Category: Kang A]]
			[[Category: Sankaran B]]

OCA at 05:07, 18 August 2021

2021-08-18T05:07:29Z

← Older revision		Revision as of 05:07, 18 August 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7rmy is ON HOLD until ~~sometime in the future~~		The entry 7rmy is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 05:10, 11 August 2021

2021-08-11T05:10:13Z

← Older revision		Revision as of 05:10, 11 August 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7rmy is ON HOLD		The entry 7rmy is ON HOLD until sometime in the future

	Authors:		Authors:

OCA: Protected "7rmy" [edit=sysop:move=sysop]

2021-08-04T09:23:20Z

Protected "7rmy" [edit=sysop:move=sysop]

← Older revision	Revision as of 09:23, 4 August 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7rmy is ON HOLD Authors: Description: Category: Unreleased Structures

2021-08-04T09:23:19Z

New page: '''Unreleased structure''' The entry 7rmy is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7rmy is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]