6yq9 - Revision history

OCA at 13:33, 24 January 2024

OCA — Wed, 24 Jan 2024 13:33:15 GMT

←Older revision		Revision as of 13:33, 24 January 2024
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	==Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol epoxide inhibitor==		==Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol epoxide inhibitor==
-	<StructureSection load='6yq9' size='340' side='right'caption='[[6yq9]]' scene=''>	+	<StructureSection load='6yq9' size='340' side='right'caption='[[6yq9]], [[Resolution\|resolution]] 1.55Å' 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=6YQ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQ9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yq9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae Aspergillus oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQ9 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=6yq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yq9 OCA], [https://pdbe.org/6yq9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yq9 RCSB], [https://www.ebi.ac.uk/pdbsum/6yq9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yq9 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]] 1.55Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5QP:(2~{R},3~{S},4~{S},5~{R},6~{S})-2-(HYDROXYMETHYL)-6-[(1~{R},2~{S},3~{R},5~{S},6~{R})-2-(HYDROXYMETHYL)-3,5,6-TRIS(OXIDANYL)CYCLOHEXYL]OXY-OXANE-3,4,5-TRIOL'>5QP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=6yq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yq9 OCA], [https://pdbe.org/6yq9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yq9 RCSB], [https://www.ebi.ac.uk/pdbsum/6yq9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yq9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1S9DH83_ASPOZ A0A1S9DH83_ASPOZ]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Amylases are key enzymes in the processing of starch in many kingdoms of life. They are important catalysts in industrial biotechnology where they are applied in, among others, food processing and the production of detergents. In man amylases are the first enzymes in the digestion of starch to glucose and arguably also the preferred target in therapeutic strategies aimed at the treatment of type 2 diabetes patients through down-tuning glucose assimilation. Efficient and sensitive assays that report selectively on retaining amylase activities irrespective of the nature and complexity of the biomaterial studied are of great value both in finding new and effective human amylase inhibitors and in the discovery of new microbial amylases with potentially advantageous features for biotechnological application. Activity-based protein profiling (ABPP) of retaining glycosidases is inherently suited for the development of such an assay format. We here report on the design and synthesis of 1,6-epi-cyclophellitol-based pseudodisaccharides equipped with a suite of reporter entities and their use in ABPP of retaining amylases from human saliva, murine tissue as well as secretomes from fungi grown on starch. The activity and efficiency of the inhibitors and probes are substantiated by extensive biochemical analysis, and the selectivity for amylases over related retaining endoglycosidases is validated by structural studies.
		+
		+	Activity-Based Protein Profiling of Retaining alpha-Amylases in Complex Biological Samples.,Chen Y, Armstrong Z, Artola M, Florea BI, Kuo CL, de Boer C, Rasmussen MS, Abou Hachem M, van der Marel GA, Codee JDC, Aerts JMFG, Davies GJ, Overkleeft HS J Am Chem Soc. 2021 Jan 26. doi: 10.1021/jacs.0c13059. PMID:33497208<ref>PMID:33497208</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yq9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Amylase 3D structures\|Amylase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspergillus oryzae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Armstrong Z]]		[[Category: Armstrong Z]]

OCA at 10:56, 10 February 2021

OCA — Wed, 10 Feb 2021 10:56:34 GMT

←Older revision		Revision as of 10:56, 10 February 2021
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-	'''Unreleased structure'''

-	~~The entry 6yq9 is ON HOLD until Paper Publication~~	+	==Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol epoxide inhibitor==
-		+	<StructureSection load='6yq9' size='340' side='right'caption='[[6yq9]]' scene=''>
-	~~Authors: Armstrong, Z., Chen, Y., Artola, M., Overkleeft, H., Davies, G.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQ9 FirstGlance]. <br>
-	~~Description:~~ Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol epoxide inhibitor	+	</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=6yq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yq9 OCA], [https://pdbe.org/6yq9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yq9 RCSB], [https://www.ebi.ac.uk/pdbsum/6yq9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yq9 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Chen~~, Y]]	+	__TOC__
-	[[Category: ~~Overkleeft, H~~]]	+	</StructureSection>
-	[[Category: Artola, M]]	+	[[Category: Large Structures]]
-	[[Category: ~~Armstrong, Z~~]]	+	[[Category: Armstrong Z]]
-	[[Category: Davies, G]]	+	[[Category: Artola M]]
		+	[[Category: Chen Y]]
		+	[[Category: Davies G]]
		+	[[Category: Overkleeft H]]

OCA at 07:32, 22 July 2020

OCA — Wed, 22 Jul 2020 07:32:06 GMT

←Older revision		Revision as of 07:32, 22 July 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6yq9 is ON HOLD	+	The entry 6yq9 is ON HOLD until Paper Publication

	Authors: Armstrong, Z., Chen, Y., Artola, M., Overkleeft, H., Davies, G.		Authors: Armstrong, Z., Chen, Y., Artola, M., Overkleeft, H., Davies, G.
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	Description: Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol epoxide inhibitor		Description: Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol epoxide inhibitor
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Artola, M]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]
	[[Category: Overkleeft, H]]		[[Category: Overkleeft, H]]
		+	[[Category: Artola, M]]
	[[Category: Armstrong, Z]]		[[Category: Armstrong, Z]]
	[[Category: Davies, G]]		[[Category: Davies, G]]

OCA: Protected "6yq9" [edit=sysop:move=sysop]

OCA — Wed, 22 Apr 2020 04:33:28 GMT

Protected "6yq9" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:33, 22 April 2020

OCA: New page: '''Unreleased structure''' The entry 6yq9 is ON HOLD Authors: Armstrong, Z., Chen, Y., Artola, M., Overkleeft, H., Davies, G. Description: Taka-amylase in complex with alpha-glucosyl e...

OCA — Wed, 22 Apr 2020 04:33:26 GMT

New page: '''Unreleased structure''' The entry 6yq9 is ON HOLD Authors: Armstrong, Z., Chen, Y., Artola, M., Overkleeft, H., Davies, G. Description: Taka-amylase in complex with alpha-glucosyl e...

New page

'''Unreleased structure'''

The entry 6yq9 is ON HOLD

Authors: Armstrong, Z., Chen, Y., Artola, M., Overkleeft, H., Davies, G.

Description: Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol epoxide inhibitor
[[Category: Unreleased Structures]]
[[Category: Artola, M]]
[[Category: Chen, Y]]
[[Category: Overkleeft, H]]
[[Category: Armstrong, Z]]
[[Category: Davies, G]]