6w70 - Revision history

OCA at 14:42, 6 March 2024

OCA — Wed, 06 Mar 2024 14:42:04 GMT

←Older revision		Revision as of 14:42, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='6w70' size='340' side='right'caption='[[6w70]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='6w70' size='340' side='right'caption='[[6w70]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6w70]] 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=6W70 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6W70 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w70]] 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=6W70 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6W70 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GG2:1-(4-METHOXYPHENYL)-7-OXO-6-[4-(2-OXOPIPERIDIN-1-YL)PHENYL]-4,5,6,7-TETRAHYDRO-1H-PYRAZOLO[3,4-C]PYRIDINE-3-CARBOXAMIDE'>GG2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.296Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6w6x\|6w6x]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GG2:1-(4-METHOXYPHENYL)-7-OXO-6-[4-(2-OXOPIPERIDIN-1-YL)PHENYL]-4,5,6,7-TETRAHYDRO-1H-PYRAZOLO[3,4-C]PYRIDINE-3-CARBOXAMIDE'>GG2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6w70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w70 OCA], [~~http~~://pdbe.org/6w70 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6w70 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6w70 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6w70 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=6w70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w70 OCA], [https://pdbe.org/6w70 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6w70 RCSB], [https://www.ebi.ac.uk/pdbsum/6w70 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6w70 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The de novo design of proteins that bind highly functionalized small molecules represents a great challenge. To enable computational design of binders, we developed a unit of protein structure-a van der Mer (vdM)-that maps the backbone of each amino acid to statistically preferred positions of interacting chemical groups. Using vdMs, we designed six de novo proteins to bind the drug apixaban; two bound with low and submicromolar affinity. X-ray crystallography and mutagenesis confirmed a structure with a precisely designed cavity that forms favorable interactions in the drug-protein complex. vdMs may enable design of functional proteins for applications in sensing, medicine, and catalysis.
-
-	A defined structural unit enables de novo design of small-molecule-binding proteins.,Polizzi NF, DeGrado WF Science. 2020 Sep 4;369(6508):1227-1233. doi: 10.1126/science.abb8330. PMID:32883865<ref>PMID:32883865</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6w70" 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: Polizzi~~, N F]]~~	+	[[Category: Polizzi NF]]
-	~~[[Category: 4-helix bundle]]~~	+
-	~~[[Category: De novo]]~~	+
-	~~[[Category: De novo protein]]~~	+
-	~~[[Category: Ligand-binding~~]]	+

OCA at 11:29, 23 September 2020

OCA — Wed, 23 Sep 2020 11:29:03 GMT

←Older revision		Revision as of 11:29, 23 September 2020
Line 1:		Line 1:

	==Crystal Structure of apixaban-bound ABLE==		==Crystal Structure of apixaban-bound ABLE==
-	<StructureSection load='6w70' size='340' side='right'caption='[[6w70]]' scene=''>	+	<StructureSection load='6w70' size='340' side='right'caption='[[6w70]], [[Resolution\|resolution]] 1.30Å' 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=6W70 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W70 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w70]] 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=6W70 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W70 FirstGlance]. <br>
-	</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=6w70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w70 OCA], [http://pdbe.org/6w70 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w70 RCSB], [http://www.ebi.ac.uk/pdbsum/6w70 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w70 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GG2:1-(4-METHOXYPHENYL)-7-OXO-6-[4-(2-OXOPIPERIDIN-1-YL)PHENYL]-4,5,6,7-TETRAHYDRO-1H-PYRAZOLO[3,4-C]PYRIDINE-3-CARBOXAMIDE'>GG2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6w6x\|6w6x]]</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=6w70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w70 OCA], [http://pdbe.org/6w70 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w70 RCSB], [http://www.ebi.ac.uk/pdbsum/6w70 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w70 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The de novo design of proteins that bind highly functionalized small molecules represents a great challenge. To enable computational design of binders, we developed a unit of protein structure-a van der Mer (vdM)-that maps the backbone of each amino acid to statistically preferred positions of interacting chemical groups. Using vdMs, we designed six de novo proteins to bind the drug apixaban; two bound with low and submicromolar affinity. X-ray crystallography and mutagenesis confirmed a structure with a precisely designed cavity that forms favorable interactions in the drug-protein complex. vdMs may enable design of functional proteins for applications in sensing, medicine, and catalysis.
		+
		+	A defined structural unit enables de novo design of small-molecule-binding proteins.,Polizzi NF, DeGrado WF Science. 2020 Sep 4;369(6508):1227-1233. doi: 10.1126/science.abb8330. PMID:32883865<ref>PMID:32883865</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6w70" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Polizzi NF]]	+	[[Category: Synthetic construct sequences]]
		+	[[Category: Polizzi, N F]]
		+	[[Category: 4-helix bundle]]
		+	[[Category: De novo]]
		+	[[Category: De novo protein]]
		+	[[Category: Ligand-binding]]

OCA at 11:16, 26 August 2020

OCA — Wed, 26 Aug 2020 11:16:47 GMT

←Older revision		Revision as of 11:16, 26 August 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6w70 ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of apixaban-bound ABLE==
-		+	<StructureSection load='6w70' size='340' side='right'caption='[[6w70]]' scene=''>
-	~~Authors~~: ~~Polizzi, N~~.F.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W70 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W70 FirstGlance]. <br>
-	~~Description~~: ~~Crystal Structure of apixaban~~-~~bound ABLE~~	+	</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=6w70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w70 OCA], [http://pdbe.org/6w70 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w70 RCSB], [http://www.ebi.ac.uk/pdbsum/6w70 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w70 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Polizzi~~, N.F~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Polizzi NF]]

OCA at 09:19, 29 July 2020

OCA — Wed, 29 Jul 2020 09:19:35 GMT

←Older revision		Revision as of 09:19, 29 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6w70 is ON HOLD	+	The entry 6w70 is ON HOLD until Paper Publication

	Authors: Polizzi, N.F.		Authors: Polizzi, N.F.

OCA: Protected "6w70" [edit=sysop:move=sysop]

OCA — Fri, 27 Mar 2020 08:27:35 GMT

Protected "6w70" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:27, 27 March 2020

OCA: New page: '''Unreleased structure''' The entry 6w70 is ON HOLD Authors: Polizzi, N.F. Description: Crystal Structure of apixaban-bound ABLE Category: Unreleased Structures [[Category: Polizz...

OCA — Fri, 27 Mar 2020 08:27:33 GMT

New page: '''Unreleased structure''' The entry 6w70 is ON HOLD Authors: Polizzi, N.F. Description: Crystal Structure of apixaban-bound ABLE Category: Unreleased Structures [[Category: Polizz...

New page

'''Unreleased structure'''

The entry 6w70 is ON HOLD

Authors: Polizzi, N.F.

Description: Crystal Structure of apixaban-bound ABLE
[[Category: Unreleased Structures]]
[[Category: Polizzi, N.F]]