2f18 - Revision history

OCA at 07:41, 23 August 2023

2023-08-23T07:41:25Z

←Older revision		Revision as of 07:41, 23 August 2023
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	==GOLGI ALPHA-MANNOSIDASE II complex with (2R,3R,4S)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidine-3,4-diol==		==GOLGI ALPHA-MANNOSIDASE II complex with (2R,3R,4S)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidine-3,4-diol==
-	<StructureSection load='2f18' size='340' side='right'caption='[[2f18]]' scene=''>	+	<StructureSection load='2f18' size='340' side='right'caption='[[2f18]], [[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=2F18 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F18 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2f18]] 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=2F18 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F18 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=2f18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f18 OCA], [https://pdbe.org/2f18 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f18 RCSB], [https://www.ebi.ac.uk/pdbsum/2f18 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f18 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]] 1.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GB1:(2R,3R,4S)-2-({[(1R)-2-HYDROXY-1-PHENYLETHYL]AMINO}METHYL)PYRROLIDINE-3,4-DIOL'>GB1</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2f18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f18 OCA], [https://pdbe.org/2f18 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f18 RCSB], [https://www.ebi.ac.uk/pdbsum/2f18 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f18 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[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).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2f18 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2f18 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Golgi alpha-mannosidase II (GMII), a zinc-dependent glycosyl hydrolase, is a promising target for drug development in anti-tumor therapies. Using X-ray crystallography, we have determined the structure of Drosophila melanogaster GMII (dGMII) complexed with three different inhibitors exhibiting IC50's ranging from 80 to 1000 microM. These structures, along with those of seven other available dGMII/inhibitor complexes, were then used as a basis for the evaluation of seven docking programs (GOLD, Glide, FlexX, AutoDock, eHiTS, LigandFit, and FITTED). We found that small inhibitors could be accurately docked by most of the software, while docking of larger compounds (i.e., those with extended aromatic cycles or long aliphatic chains) was more problematic. Overall, Glide provided the best docking results, with the most accurately predicted binding around the active site zinc atom. Further evaluation of Glide's performance revealed its ability to extract active compounds from a benchmark library of decoys.
		+
		+	Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography.,Englebienne P, Fiaux H, Kuntz DA, Corbeil CR, Gerber-Lemaire S, Rose DR, Moitessier N Proteins. 2007 Oct 1;69(1):160-76. PMID:17557336<ref>PMID:17557336</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 2f18" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Mannosidase 3D structures\|Mannosidase 3D structures]]		*[[Mannosidase 3D structures\|Mannosidase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Drosophila melanogaster]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kuntz DA]]		[[Category: Kuntz DA]]
	[[Category: Rose DR]]		[[Category: Rose DR]]

OCA at 10:36, 17 February 2021

2021-02-17T10:36:48Z

←Older revision		Revision as of 10:36, 17 February 2021
Line 1:		Line 1:

	==GOLGI ALPHA-MANNOSIDASE II complex with (2R,3R,4S)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidine-3,4-diol==		==GOLGI ALPHA-MANNOSIDASE II complex with (2R,3R,4S)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidine-3,4-diol==
-	<StructureSection load='2f18' size='340' side='right' caption='[[2f18]]~~, [[Resolution\|resolution]] 1.30Å~~' scene=''>	+	<StructureSection load='2f18' size='340' side='right'caption='[[2f18]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[2f18]] 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=2F18 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2F18 FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F18 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F18 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GB1:(2R,3R,4S)-2-({[(1R)-2-HYDROXY-1-PHENYLETHYL]AMINO}METHYL)PYRROLIDINE-3,4-DIOL'>GB1</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=2f18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f18 OCA], [https://pdbe.org/2f18 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f18 RCSB], [https://www.ebi.ac.uk/pdbsum/2f18 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f18 ProSAT]</span></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hty\|1hty]], [[1hww\|1hww]], [[1hxk\|1hxk]], [[1ps2\|1ps2]], [[1qwn\|1qwn]], [[1qx1\|1qx1]], [[1r33\|1r33]], [[1r34\|1r34]], [[1tqs\|1tqs]], [[1tqt\|1tqt]], [[1tqu\|1tqu]], [[1tqv\|1tqv]], [[1tqw\|1tqw]], [[2alw\|2alw]], [[2f1a\|2f1a]], [[2f1b\|2f1b]]</td></tr>	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alpha-Man-II, GmII ([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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2f18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f18 OCA], [~~http~~://pdbe.org/2f18 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2f18 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2f18 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2f18 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 20:		Line 16:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2f18 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2f18 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Golgi alpha-mannosidase II (GMII), a zinc-dependent glycosyl hydrolase, is a promising target for drug development in anti-tumor therapies. Using X-ray crystallography, we have determined the structure of Drosophila melanogaster GMII (dGMII) complexed with three different inhibitors exhibiting IC50's ranging from 80 to 1000 microM. These structures, along with those of seven other available dGMII/inhibitor complexes, were then used as a basis for the evaluation of seven docking programs (GOLD, Glide, FlexX, AutoDock, eHiTS, LigandFit, and FITTED). We found that small inhibitors could be accurately docked by most of the software, while docking of larger compounds (i.e., those with extended aromatic cycles or long aliphatic chains) was more problematic. Overall, Glide provided the best docking results, with the most accurately predicted binding around the active site zinc atom. Further evaluation of Glide's performance revealed its ability to extract active compounds from a benchmark library of decoys.
-
-	Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography.,Englebienne P, Fiaux H, Kuntz DA, Corbeil CR, Gerber-Lemaire S, Rose DR, Moitessier N Proteins. 2007 Oct 1;69(1):160-76. PMID:17557336<ref>PMID:17557336</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2f18" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Mannosidase\|Mannosidase]]	+	*[[Mannosidase 3D structures\|Mannosidase 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Drome]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase~~]]	+	[[Category: Kuntz DA]]
-	[[Category: Kuntz~~, D A~~]]	+	[[Category: Rose DR]]
-	[[Category: Rose~~, D R]]~~	+
-	~~[[Category: Glycosyl hydrolase family 38]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 09:11, 14 June 2018

2018-06-14T09:11:10Z

←Older revision		Revision as of 09:11, 14 June 2018
Line 1:		Line 1:
		+
	==GOLGI ALPHA-MANNOSIDASE II complex with (2R,3R,4S)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidine-3,4-diol==		==GOLGI ALPHA-MANNOSIDASE II complex with (2R,3R,4S)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidine-3,4-diol==
	<StructureSection load='2f18' size='340' side='right' caption='[[2f18]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='2f18' size='340' side='right' caption='[[2f18]], [[Resolution\|resolution]] 1.30Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alpha-Man-II, GmII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alpha-Man-II, GmII ([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='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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f18 OCA], [http://pdbe.org/2f18 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f18 RCSB], [http://www.ebi.ac.uk/pdbsum/2f18 PDBsum]</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=2f18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f18 OCA], [http://pdbe.org/2f18 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f18 RCSB], [http://www.ebi.ac.uk/pdbsum/2f18 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2f18 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f1/2f18_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f1/2f18_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 13:47, 9 February 2016

2016-02-09T13:47:49Z

←Older revision		Revision as of 13:47, 9 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2f18 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:49, 10 September 2015

2015-09-10T22:49:47Z

←Older revision		Revision as of 22:49, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2f18' size='340' side='right' caption='[[2f18]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='2f18' size='340' side='right' caption='[[2f18]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2f18]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Drosophila_melanogaster Drosophila melanogaster~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F18 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F18 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2f18]] 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=2F18 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F18 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GB1:(2R,3R,4S)-2-({[(1R)-2-HYDROXY-1-PHENYLETHYL]AMINO}METHYL)PYRROLIDINE-3,4-DIOL'>GB1</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GB1:(2R,3R,4S)-2-({[(1R)-2-HYDROXY-1-PHENYLETHYL]AMINO}METHYL)PYRROLIDINE-3,4-DIOL'>GB1</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hty\|1hty]], [[1hww\|1hww]], [[1hxk\|1hxk]], [[1ps2\|1ps2]], [[1qwn\|1qwn]], [[1qx1\|1qx1]], [[1r33\|1r33]], [[1r34\|1r34]], [[1tqs\|1tqs]], [[1tqt\|1tqt]], [[1tqu\|1tqu]], [[1tqv\|1tqv]], [[1tqw\|1tqw]], [[2alw\|2alw]], [[2f1a\|2f1a]], [[2f1b\|2f1b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hty\|1hty]], [[1hww\|1hww]], [[1hxk\|1hxk]], [[1ps2\|1ps2]], [[1qwn\|1qwn]], [[1qx1\|1qx1]], [[1r33\|1r33]], [[1r34\|1r34]], [[1tqs\|1tqs]], [[1tqt\|1tqt]], [[1tqu\|1tqu]], [[1tqv\|1tqv]], [[1tqw\|1tqw]], [[2alw\|2alw]], [[2f1a\|2f1a]], [[2f1b\|2f1b]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alpha-Man-II, GmII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 ~~Drosophila melanogaster~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alpha-Man-II, GmII ([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='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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f18 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f18 RCSB], [http://www.ebi.ac.uk/pdbsum/2f18 PDBsum]</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=2f18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f18 OCA], [http://pdbe.org/2f18 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f18 RCSB], [http://www.ebi.ac.uk/pdbsum/2f18 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2f18" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Drosophila melanogaster~~]]	+	[[Category: Drome]]
	[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]		[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]
	[[Category: Kuntz, D A]]		[[Category: Kuntz, D A]]

OCA at 16:56, 15 January 2015

2015-01-15T16:56:53Z

←Older revision		Revision as of 16:56, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2f18]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F18 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F18 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2f18]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F18 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F18 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GB1:(2R,3R,4S)-2-({[(1R)-2-HYDROXY-1-PHENYLETHYL]AMINO}METHYL)PYRROLIDINE-3,4-DIOL'>GB1</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GB1:(2R,3R,4S)-2-({[(1R)-2-HYDROXY-1-PHENYLETHYL]AMINO}METHYL)PYRROLIDINE-3,4-DIOL'>GB1</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hty\|1hty]], [[1hww\|1hww]], [[1hxk\|1hxk]], [[1ps2\|1ps2]], [[1qwn\|1qwn]], [[1qx1\|1qx1]], [[1r33\|1r33]], [[1r34\|1r34]], [[1tqs\|1tqs]], [[1tqt\|1tqt]], [[1tqu\|1tqu]], [[1tqv\|1tqv]], [[1tqw\|1tqw]], [[2alw\|2alw]], [[2f1a\|2f1a]], [[2f1b\|2f1b]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hty\|1hty]], [[1hww\|1hww]], [[1hxk\|1hxk]], [[1ps2\|1ps2]], [[1qwn\|1qwn]], [[1qx1\|1qx1]], [[1r33\|1r33]], [[1r34\|1r34]], [[1tqs\|1tqs]], [[1tqt\|1tqt]], [[1tqu\|1tqu]], [[1tqv\|1tqv]], [[1tqw\|1tqw]], [[2alw\|2alw]], [[2f1a\|2f1a]], [[2f1b\|2f1b]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alpha-Man-II, GmII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alpha-Man-II, GmII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])</td></tr>
-	<tr><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='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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f18 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f18 RCSB], [http://www.ebi.ac.uk/pdbsum/2f18 PDBsum]</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=2f18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f18 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f18 RCSB], [http://www.ebi.ac.uk/pdbsum/2f18 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Drosophila melanogaster]]		[[Category: Drosophila melanogaster]]
	[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]		[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]
-	[[Category: Kuntz, D A.]]	+	[[Category: Kuntz, D A]]
-	[[Category: Rose, D R.]]	+	[[Category: Rose, D R]]
	[[Category: Glycosyl hydrolase family 38]]		[[Category: Glycosyl hydrolase family 38]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 02:32, 29 September 2014

2014-09-29T02:32:46Z

←Older revision		Revision as of 02:32, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2f18.~~png~~\|~~left~~\|200px]]	+	==GOLGI ALPHA-MANNOSIDASE II complex with (2R,3R,4S)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidine-3,4-diol==
		+	<StructureSection load='2f18' size='340' side='right' caption='[[2f18]], [[Resolution\|resolution]] 1.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2f18]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F18 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F18 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GB1:(2R,3R,4S)-2-({[(1R)-2-HYDROXY-1-PHENYLETHYL]AMINO}METHYL)PYRROLIDINE-3,4-DIOL'>GB1</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hty\|1hty]], [[1hww\|1hww]], [[1hxk\|1hxk]], [[1ps2\|1ps2]], [[1qwn\|1qwn]], [[1qx1\|1qx1]], [[1r33\|1r33]], [[1r34\|1r34]], [[1tqs\|1tqs]], [[1tqt\|1tqt]], [[1tqu\|1tqu]], [[1tqv\|1tqv]], [[1tqw\|1tqw]], [[2alw\|2alw]], [[2f1a\|2f1a]], [[2f1b\|2f1b]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alpha-Man-II, GmII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 Drosophila melanogaster])</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2f18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f18 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2f18 RCSB], [http://www.ebi.ac.uk/pdbsum/2f18 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f1/2f18_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Golgi alpha-mannosidase II (GMII), a zinc-dependent glycosyl hydrolase, is a promising target for drug development in anti-tumor therapies. Using X-ray crystallography, we have determined the structure of Drosophila melanogaster GMII (dGMII) complexed with three different inhibitors exhibiting IC50's ranging from 80 to 1000 microM. These structures, along with those of seven other available dGMII/inhibitor complexes, were then used as a basis for the evaluation of seven docking programs (GOLD, Glide, FlexX, AutoDock, eHiTS, LigandFit, and FITTED). We found that small inhibitors could be accurately docked by most of the software, while docking of larger compounds (i.e., those with extended aromatic cycles or long aliphatic chains) was more problematic. Overall, Glide provided the best docking results, with the most accurately predicted binding around the active site zinc atom. Further evaluation of Glide's performance revealed its ability to extract active compounds from a benchmark library of decoys.

-	~~{{STRUCTURE_2f18\| PDB=2f18 \| SCENE= }}~~	+	Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography.,Englebienne P, Fiaux H, Kuntz DA, Corbeil CR, Gerber-Lemaire S, Rose DR, Moitessier N Proteins. 2007 Oct 1;69(1):160-76. PMID:17557336<ref>PMID:17557336</ref>

-	~~===GOLGI ALPHA-MANNOSIDASE II complex with (2R~~,~~3R,4S)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidine-3,4-diol===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17557336}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2f18]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Drosophila_melanogaster Drosophila melanogaster]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2F18 OCA].~~	+

	==See Also==		==See Also==
	*[[Mannosidase\|Mannosidase]]		*[[Mannosidase\|Mannosidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:017557336<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Drosophila melanogaster]]		[[Category: Drosophila melanogaster]]
	[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]		[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]

OCA at 14:02, 20 October 2012

2012-10-20T14:02:19Z

←Older revision		Revision as of 14:02, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2f18]] is a 1 chain structure ~~of [[Mannosidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F18 OCA].	+	[[2f18]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F18 OCA].

	==See Also==		==See Also==

OCA: Protected "2f18" [edit=sysop:move=sysop]

2012-07-26T13:51:36Z

Protected "2f18" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:51, 26 July 2012

OCA at 13:51, 26 July 2012

2012-07-26T13:51:34Z

←Older revision		Revision as of 13:51, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2f18.png\|left\|200px]]		[[Image:2f18.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2f18", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2f18\| PDB=2f18 \| SCENE= }}		{{STRUCTURE_2f18\| PDB=2f18 \| SCENE= }}

	===GOLGI ALPHA-MANNOSIDASE II complex with (2R,3R,4S)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidine-3,4-diol===		===GOLGI ALPHA-MANNOSIDASE II complex with (2R,3R,4S)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidine-3,4-diol===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17557336}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17557336 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17557336}}		{{ABSTRACT_PUBMED_17557336}}

	==About this Structure==		==About this Structure==
-	~~2F18~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F18 OCA].	+	[[2f18]] is a 1 chain structure of [[Mannosidase]] with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F18 OCA].
		+
		+	==See Also==
		+	*[[Mannosidase\|Mannosidase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17557336~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017557336</ref><references group="xtra"/>
	[[Category: Drosophila melanogaster]]		[[Category: Drosophila melanogaster]]
	[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]		[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]
Line 29:		Line 20:
	[[Category: Rose, D R.]]		[[Category: Rose, D R.]]
	[[Category: Glycosyl hydrolase family 38]]		[[Category: Glycosyl hydrolase family 38]]
-		+	[[Category: Hydrolase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 10:14:40 2009''~~	+