6rrw - Revision history

OCA at 12:27, 24 January 2024

OCA — Wed, 24 Jan 2024 12:27:13 GMT

←Older revision		Revision as of 12:27, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6rrw' size='340' side='right'caption='[[6rrw]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='6rrw' size='340' side='right'caption='[[6rrw]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rrw]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Drome Drome~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RRW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6RRW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rrw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RRW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RRW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KG5:(2~{R},3~{R},4~{R},5~{S})-1-[5-[[4-(3,4-dihydro-2~{H}-1,5-benzodioxepin-7-yl)phenyl]methoxy]pentyl]-2-(hydroxymethyl)piperidine-3,4,5-triol'>KG5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.15Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alpha-Man-IIa, GmII, CG18802 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KG5:(2~{R},3~{R},4~{R},5~{S})-1-[5-[[4-(3,4-dihydro-2~{H}-1,5-benzodioxepin-7-yl)phenyl]methoxy]pentyl]-2-(hydroxymethyl)piperidine-3,4,5-triol'>KG5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannosyl-oligosaccharide_1,3-1,6-alpha-mannosidase Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.114 3.2.1.114] </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=6rrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rrw OCA], [https://pdbe.org/6rrw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rrw RCSB], [https://www.ebi.ac.uk/pdbsum/6rrw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rrw ProSAT]</span></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=6rrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rrw OCA], [~~http~~://pdbe.org/6rrw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6rrw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6rrw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6rrw ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MAN2_DROME MAN2_DROME]] Catalyzes the first committed step in the biosynthesis of complex N-glycans. It controls conversion of high mannose to complex N-glycans; the final hydrolytic step in the N-glycan maturation pathway (By similarity).	+	[https://www.uniprot.org/uniprot/MAN2_DROME MAN2_DROME] Catalyzes the first committed step in the biosynthesis of complex N-glycans. It controls conversion of high mannose to complex N-glycans; the final hydrolytic step in the N-glycan maturation pathway (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Drome~~]]	+	[[Category: Drosophila melanogaster]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]~~	+	[[Category: Aerts JMFG]]
-	[[Category: Aerts~~, J M.F G~~]]	+	[[Category: Armstrong Z]]
-	[[Category: Armstrong, Z]]	+	[[Category: Beenakker TJM]]
-	[[Category: Beenakker~~, T J.M]]~~	+	[[Category: Codee JDC]]
-	~~[[Category: Boer, C de~~]]	+	[[Category: Davies GJ]]
-	[[Category: Codee~~, J D.C~~]]	+	[[Category: Debets M]]
-	[[Category: Davies~~, G J~~]]	+	[[Category: Geurink PP]]
-	[[Category: Debets, M]]	+	[[Category: Johnson R]]
-	[[Category: Geurink~~, P P~~]]	+	[[Category: Kuo CL]]
-	[[Category: Johnson, R]]	+	[[Category: Lahav D]]
-	[[Category: Kuo~~, C L~~]]	+	[[Category: Ovaa H]]
-	[[Category: Lahav, D]]	+	[[Category: Overkleeft HS]]
-	[[Category: Ovaa, H]]	+	[[Category: Wong CS]]
-	[[Category: Overkleeft~~, H S]]~~	+	[[Category: Wu L]]
-	~~[[Category: Rijssel, E R.van]]~~	+	[[Category: De Boer C]]
-	~~[[Category: Stelt, M van der~~]]	+	[[Category: Van Rijssel ER]]
-	[[Category: Wong~~, C S~~]]	+	[[Category: Van der Stelt M]]
-	[[Category: Wu, L]]	+
-	[[Category: ~~Glycoside hydrolase~~]]	+
-	[[Category: ~~Hydrolase~~]]	+
-	[[Category: ~~Mannosidase~~]]	+

OCA at 08:19, 20 January 2021

OCA — Wed, 20 Jan 2021 08:19:30 GMT

←Older revision		Revision as of 08:19, 20 January 2021
Line 1:		Line 1:

	==GOLGI ALPHA-MANNOSIDASE II in complex with (2R,3R,4R,5S)-1-(5-{[4-(3,4-Dihydro-2H-1,5-benzodioxepin-7-yl)benzyl]oxy}pentyl)-2-(hydroxymethyl)-3,4,5-piperidinetriol==		==GOLGI ALPHA-MANNOSIDASE II in complex with (2R,3R,4R,5S)-1-(5-{[4-(3,4-Dihydro-2H-1,5-benzodioxepin-7-yl)benzyl]oxy}pentyl)-2-(hydroxymethyl)-3,4,5-piperidinetriol==
-	<StructureSection load='6rrw' size='340' side='right'caption='[[6rrw]]' scene=''>	+	<StructureSection load='6rrw' size='340' side='right'caption='[[6rrw]], [[Resolution\|resolution]] 2.15Å' 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=6RRW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6RRW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rrw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RRW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6RRW 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=6rrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rrw OCA], [http://pdbe.org/6rrw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rrw RCSB], [http://www.ebi.ac.uk/pdbsum/6rrw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rrw 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=KG5:(2~{R},3~{R},4~{R},5~{S})-1-[5-[[4-(3,4-dihydro-2~{H}-1,5-benzodioxepin-7-yl)phenyl]methoxy]pentyl]-2-(hydroxymethyl)piperidine-3,4,5-triol'>KG5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alpha-Man-IIa, GmII, CG18802 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannosyl-oligosaccharide_1,3-1,6-alpha-mannosidase Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.114 3.2.1.114] </span></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=6rrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rrw OCA], [http://pdbe.org/6rrw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rrw RCSB], [http://www.ebi.ac.uk/pdbsum/6rrw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rrw ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MAN2_DROME MAN2_DROME]] Catalyzes the first committed step in the biosynthesis of complex N-glycans. It controls conversion of high mannose to complex N-glycans; the final hydrolytic step in the N-glycan maturation pathway (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Golgi mannosidase II (GMII) catalyzes the sequential hydrolysis of two mannosyl residues from GlcNAcMan5GlcNAc2 to produce GlcNAcMan3GlcNAc2, the precursor for all complex N-glycans, including the branched N-glycans associated with cancer. Inhibitors of GMII are potential cancer therapeutics, but their usefulness is limited by off-target effects, which produce alpha-mannosidosis-like symptoms. Despite many structural and mechanistic studies of GMII, we still lack a potent and selective inhibitor of this enzyme. Here, we synthesized manno-epi-cyclophellitol epoxide and aziridines and demonstrate their covalent modification and time-dependent inhibition of GMII. Application of fluorescent manno-epi-cyclophellitol aziridine derivatives enabled activity-based protein profiling of alpha-mannosidases from both human cell lysate and mouse tissue extracts. Synthesized probes also facilitated a fluorescence polarization-based screen for dGMII inhibitors. We identified seven previously unknown inhibitors of GMII from a library of over 350 iminosugars and investigated their binding modalities through X-ray crystallography. Our results reveal previously unobserved inhibitor binding modes and promising scaffolds for the generation of selective GMII inhibitors.
		+
		+	Manno-epi-cyclophellitols Enable Activity-Based Protein Profiling of Human alpha-Mannosidases and Discovery of New Golgi Mannosidase II Inhibitors.,Armstrong Z, Kuo CL, Lahav D, Liu B, Johnson R, Beenakker TJM, de Boer C, Wong CS, van Rijssel ER, Debets MF, Florea BI, Hissink C, Boot RG, Geurink PP, Ovaa H, van der Stelt M, van der Marel GM, Codee JDC, Aerts JMFG, Wu L, Overkleeft HS, Davies GJ J Am Chem Soc. 2020 Jul 29;142(30):13021-13029. doi: 10.1021/jacs.0c03880. Epub, 2020 Jul 16. PMID:32605368<ref>PMID:32605368</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6rrw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Mannosidase 3D structures\|Mannosidase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Drome]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aerts ~~JMFG~~]]	+	[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]
-	[[Category: Armstrong Z]]	+	[[Category: Aerts, J M.F G]]
-	[[Category: Beenakker ~~TJM~~]]	+	[[Category: Armstrong, Z]]
-	[[Category: Codee ~~JDC~~]]	+	[[Category: Beenakker, T J.M]]
-	[[Category: Davies GJ]]	+	[[Category: Boer, C de]]
-	[[Category: Debets M]]	+	[[Category: Codee, J D.C]]
-	[[Category: Geurink PP]]	+	[[Category: Davies, G J]]
-	[[Category: Johnson R]]	+	[[Category: Debets, M]]
-	[[Category: Kuo CL]]	+	[[Category: Geurink, P P]]
-	[[Category: Lahav D]]	+	[[Category: Johnson, R]]
-	[[Category: Ovaa H]]	+	[[Category: Kuo, C L]]
-	[[Category: Overkleeft HS]]	+	[[Category: Lahav, D]]
-	[[Category: Wong CS]]	+	[[Category: Ovaa, H]]
-	[[Category: Wu L]]	+	[[Category: Overkleeft, H S]]
-	[[Category: ~~De Boer C~~]]	+	[[Category: Rijssel, E R.van]]
-	[[Category: ~~Van Rijssel ER~~]]	+	[[Category: Stelt, M van der]]
-	[[Category: ~~Van der Stelt M~~]]	+	[[Category: Wong, C S]]
		+	[[Category: Wu, L]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mannosidase]]

OCA at 14:02, 8 July 2020

OCA — Wed, 08 Jul 2020 14:02:37 GMT

←Older revision		Revision as of 14:02, 8 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6rrw is ~~ON HOLD until Paper Publication~~	+	==GOLGI ALPHA-MANNOSIDASE II in complex with (2R,3R,4R,5S)-1-(5-{[4-(3,4-Dihydro-2H-1,5-benzodioxepin-7-yl)benzyl]oxy}pentyl)-2-(hydroxymethyl)-3,4,5-piperidinetriol==
-		+	<StructureSection load='6rrw' size='340' side='right'caption='[[6rrw]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RRW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6RRW FirstGlance]. <br>
-	~~Description~~:	+	</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=6rrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rrw OCA], [http://pdbe.org/6rrw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rrw RCSB], [http://www.ebi.ac.uk/pdbsum/6rrw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rrw ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Aerts JMFG]]
		+	[[Category: Armstrong Z]]
		+	[[Category: Beenakker TJM]]
		+	[[Category: Codee JDC]]
		+	[[Category: Davies GJ]]
		+	[[Category: Debets M]]
		+	[[Category: Geurink PP]]
		+	[[Category: Johnson R]]
		+	[[Category: Kuo CL]]
		+	[[Category: Lahav D]]
		+	[[Category: Ovaa H]]
		+	[[Category: Overkleeft HS]]
		+	[[Category: Wong CS]]
		+	[[Category: Wu L]]
		+	[[Category: De Boer C]]
		+	[[Category: Van Rijssel ER]]
		+	[[Category: Van der Stelt M]]

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

OCA — Wed, 29 May 2019 04:44:59 GMT

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

←Older revision

Revision as of 04:44, 29 May 2019

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

OCA — Wed, 29 May 2019 04:44:58 GMT

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

New page

'''Unreleased structure'''

The entry 6rrw is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]