1fhd - Revision history

OCA at 10:14, 20 March 2024

OCA — Wed, 20 Mar 2024 10:14:51 GMT

←Older revision		Revision as of 10:14, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='1fhd' size='340' side='right'caption='[[1fhd]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1fhd' size='340' side='right'caption='[[1fhd]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1fhd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacterium_fimi"_mcbeth_and_scales_1913 "bacterium~~ fimi~~" mcbeth and scales 1913~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FHD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1fhd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellulomonas_fimi Cellulomonas fimi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FHD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=XIM:5~~,~~6,7,8-TETRAHYDRO-IMIDAZO~~[1~~,2-A]PYRIDINE-6,7,8-TRIOL'>XIM</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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]] 1.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;'>[[2exo\|2exo]]~~, ~~[[1exp\|1exp]]~~, ~~[[1xyl\|1xyl]]~~, [~~[1fh7\|1fh7]]~~, ~~[[1fh8\|1fh8]~~], ~~[[1fh9\|1fh9]]</div~~></td><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XIM:5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>XIM</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase_(non-reducing_end) Cellulose 1,4-beta-cellobiosidase (non-reducing end)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </~~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=1fhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fhd OCA], [https://pdbe.org/1fhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fhd RCSB], [https://www.ebi.ac.uk/pdbsum/1fhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fhd 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=1fhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fhd OCA], [https://pdbe.org/1fhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fhd RCSB], [https://www.ebi.ac.uk/pdbsum/1fhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fhd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GUX_CELFI GUX_CELFI] Hydrolyzes both cellulose and xylan. Has also weak endoglucanase activity. The biological conversion of cellulose to glucose generally requires three types of hydrolytic enzymes: (1) Endoglucanases which cut internal beta-1,4-glucosidic bonds; (2) Exocellobiohydrolases that cut the dissaccharide cellobiose from the non-reducing end of the cellulose polymer chain; (3) Beta-1,4-glucosidases which hydrolyze the cellobiose and other short cello-oligosaccharides to glucose.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1fhd 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=1fhd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Detailed insights into the mode of binding of a series of tight-binding aza-sugar glycosidase inhibitors of two fundamentally different classes are described through X-ray crystallographic studies of complexes with the retaining family 10 xylanase Cex from Cellulomonas fimi. Complexes with xylobiose-derived aza-sugar inhibitors of the substituted "amidine" class (xylobio-imidazole, K(i) = 150 nM; xylobio-lactam oxime, K(i) = 370 nM) reveal lateral interaction of the "glycosidic" nitrogen with the acid/base catalyst (Glu127) and hydrogen bonding of the sugar 2-hydroxyl with the catalytic nucleophile (Glu233), as expected. Tight binding of xylobio-isofagomine (K(i) = 130 nM) appears to be a consequence of strong interactions of the ring nitrogen with the catalytic nucleophile while, surprisingly, no direct protein contacts are made with the ring nitrogen of the xylobio-deoxynojirimycin analogue (K(i) = 5800 nM). Instead the nitrogen interacts with two ordered water molecules, thereby accounting for its relatively weaker binding, though it still binds some 1200-fold more tightly than does xylobiose, presumably as a consequence of electrostatic interactions at the active site. Dramatically weaker binding of these same inhibitors to the family 11 xylanase Bcx from Bacillus circulans (K(i) from 0.5 to 1.5 mM) is rationalized for the substituted amidines on the basis that this enzyme utilizes a syn protonation trajectory and likely hydrolyzes via a (2,5)B boat transition state. Weaker binding of the deoxynojirimycin and isofagomine analogues likely reflects the energetic penalty for distortion of these analogues to a (2,5)B conformation, possibly coupled with destabilizing interactions with Tyr69, a conserved, catalytically essential active site residue.
-
-	Detailed structural analysis of glycosidase/inhibitor interactions: complexes of Cex from Cellulomonas fimi with xylobiose-derived aza-sugars.,Notenboom V, Williams SJ, Hoos R, Withers SG, Rose DR Biochemistry. 2000 Sep 26;39(38):11553-63. PMID:10995222<ref>PMID:10995222</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1fhd" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacterium~~ fimi ~~mcbeth and scales 1913~~]]	+	[[Category: Cellulomonas fimi]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hoos, R]]	+	[[Category: Hoos R]]
-	[[Category: Notenboom, V]]	+	[[Category: Notenboom V]]
-	[[Category: Rose~~, D R~~]]	+	[[Category: Rose DR]]
-	[[Category: Williams~~, S J~~]]	+	[[Category: Williams SJ]]
-	[[Category: Withers~~, S G]]~~	+	[[Category: Withers SG]]
-	~~[[Category: Catalytic mechanism]]~~	+
-	~~[[Category: Glycosyl hydrolase family 10]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Xylanase~~]]	+

OCA at 11:09, 28 July 2021

OCA — Wed, 28 Jul 2021 11:09:48 GMT

←Older revision		Revision as of 11:09, 28 July 2021
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	<StructureSection load='1fhd' size='340' side='right'caption='[[1fhd]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1fhd' size='340' side='right'caption='[[1fhd]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1fhd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacterium_fimi"_mcbeth_and_scales_1913 "bacterium fimi" mcbeth and scales 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1FHD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1fhd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_fimi"_mcbeth_and_scales_1913 "bacterium fimi" mcbeth and scales 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FHD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XIM:5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>XIM</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XIM:5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>XIM</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exo\|2exo]], [[1exp\|1exp]], [[1xyl\|1xyl]], [[1fh7\|1fh7]], [[1fh8\|1fh8]], [[1fh9\|1fh9]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2exo\|2exo]], [[1exp\|1exp]], [[1xyl\|1xyl]], [[1fh7\|1fh7]], [[1fh8\|1fh8]], [[1fh9\|1fh9]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase_(non-reducing_end) Cellulose 1,4-beta-cellobiosidase (non-reducing end)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase_(non-reducing_end) Cellulose 1,4-beta-cellobiosidase (non-reducing end)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </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=1fhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fhd OCA], [~~http~~://pdbe.org/1fhd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1fhd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1fhd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1fhd 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=1fhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fhd OCA], [https://pdbe.org/1fhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fhd RCSB], [https://www.ebi.ac.uk/pdbsum/1fhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fhd ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 09:05, 23 October 2019

OCA — Wed, 23 Oct 2019 09:05:33 GMT

←Older revision		Revision as of 09:05, 23 October 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF THE XYLANASE CEX WITH XYLOBIOSE-DERIVED IMIDAZOLE INHIBITOR==		==CRYSTAL STRUCTURE OF THE XYLANASE CEX WITH XYLOBIOSE-DERIVED IMIDAZOLE INHIBITOR==
-	<StructureSection load='1fhd' size='340' side='right' caption='[[1fhd]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1fhd' size='340' side='right'caption='[[1fhd]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1fhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_fimi"_mcbeth_and_scales_1913 "bacterium fimi" mcbeth and scales 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FHD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_fimi"_mcbeth_and_scales_1913 "bacterium fimi" mcbeth and scales 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FHD FirstGlance]. <br>
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Bacterium fimi mcbeth and scales 1913]]		[[Category: Bacterium fimi mcbeth and scales 1913]]
		+	[[Category: Large Structures]]
	[[Category: Hoos, R]]		[[Category: Hoos, R]]
	[[Category: Notenboom, V]]		[[Category: Notenboom, V]]

OCA at 09:27, 27 December 2017

OCA — Wed, 27 Dec 2017 09:27:44 GMT

←Older revision		Revision as of 09:27, 27 December 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF THE XYLANASE CEX WITH XYLOBIOSE-DERIVED IMIDAZOLE INHIBITOR==		==CRYSTAL STRUCTURE OF THE XYLANASE CEX WITH XYLOBIOSE-DERIVED IMIDAZOLE INHIBITOR==
	<StructureSection load='1fhd' size='340' side='right' caption='[[1fhd]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1fhd' size='340' side='right' caption='[[1fhd]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1fhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_fimi"_mcbeth_and_scales_1913 "bacterium fimi" mcbeth and scales 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FHD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_fimi"_mcbeth_and_scales_1913 "bacterium fimi" mcbeth and scales 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FHD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XIM:5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>XIM</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=XIM:5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>XIM</scene></td></tr>	+
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exo\|2exo]], [[1exp\|1exp]], [[1xyl\|1xyl]], [[1fh7\|1fh7]], [[1fh8\|1fh8]], [[1fh9\|1fh9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exo\|2exo]], [[1exp\|1exp]], [[1xyl\|1xyl]], [[1fh7\|1fh7]], [[1fh8\|1fh8]], [[1fh9\|1fh9]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase_(non-reducing_end) Cellulose 1,4-beta-cellobiosidase (non-reducing end)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase_(non-reducing_end) Cellulose 1,4-beta-cellobiosidase (non-reducing end)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </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=1fhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fhd OCA], [http://pdbe.org/1fhd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fhd RCSB], [http://www.ebi.ac.uk/pdbsum/1fhd 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=1fhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fhd OCA], [http://pdbe.org/1fhd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fhd RCSB], [http://www.ebi.ac.uk/pdbsum/1fhd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1fhd ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fh/1fhd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fh/1fhd_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 04:59, 9 February 2016

OCA — Tue, 09 Feb 2016 04:59:03 GMT

←Older revision		Revision as of 04:59, 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=1fhd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 18:51, 10 September 2015

OCA — Thu, 10 Sep 2015 18:51:42 GMT

←Older revision		Revision as of 18:51, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1fhd' size='340' side='right' caption='[[1fhd]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1fhd' size='340' side='right' caption='[[1fhd]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1fhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Cellulomonas_fimi Cellulomonas~~ fimi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FHD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1fhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_fimi"_mcbeth_and_scales_1913 "bacterium fimi" mcbeth and scales 1913]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FHD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=XIM:5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>XIM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=XIM:5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>XIM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exo\|2exo]], [[1exp\|1exp]], [[1xyl\|1xyl]], [[1fh7\|1fh7]], [[1fh8\|1fh8]], [[1fh9\|1fh9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exo\|2exo]], [[1exp\|1exp]], [[1xyl\|1xyl]], [[1fh7\|1fh7]], [[1fh8\|1fh8]], [[1fh9\|1fh9]]</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulose_1,4-beta-~~cellobiosidase~~ Cellulose 1,4-beta-cellobiosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase_(non-reducing_end) Cellulose 1,4-beta-cellobiosidase (non-reducing end)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </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=1fhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fhd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fhd RCSB], [http://www.ebi.ac.uk/pdbsum/1fhd 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=1fhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fhd OCA], [http://pdbe.org/1fhd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fhd RCSB], [http://www.ebi.ac.uk/pdbsum/1fhd 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 1fhd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cellulomonas~~ fimi]]	+	[[Category: Bacterium fimi mcbeth and scales 1913]]
-	~~[[Category: Cellulose 1,4-beta-cellobiosidase~~]]	+
	[[Category: Hoos, R]]		[[Category: Hoos, R]]
	[[Category: Notenboom, V]]		[[Category: Notenboom, V]]

OCA at 21:31, 22 December 2014

OCA — Mon, 22 Dec 2014 21:31:41 GMT

←Older revision		Revision as of 21:31, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1fhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cellulomonas_fimi Cellulomonas fimi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FHD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cellulomonas_fimi Cellulomonas fimi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FHD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=XIM:5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>XIM</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=XIM:5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>XIM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exo\|2exo]], [[1exp\|1exp]], [[1xyl\|1xyl]], [[1fh7\|1fh7]], [[1fh8\|1fh8]], [[1fh9\|1fh9]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exo\|2exo]], [[1exp\|1exp]], [[1xyl\|1xyl]], [[1fh7\|1fh7]], [[1fh8\|1fh8]], [[1fh9\|1fh9]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase Cellulose 1,4-beta-cellobiosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase Cellulose 1,4-beta-cellobiosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </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=1fhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fhd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fhd RCSB], [http://www.ebi.ac.uk/pdbsum/1fhd 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=1fhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fhd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fhd RCSB], [http://www.ebi.ac.uk/pdbsum/1fhd 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 33:		Line 33:
	[[Category: Cellulomonas fimi]]		[[Category: Cellulomonas fimi]]
	[[Category: Cellulose 1,4-beta-cellobiosidase]]		[[Category: Cellulose 1,4-beta-cellobiosidase]]
-	[[Category: Hoos, R.]]	+	[[Category: Hoos, R]]
-	[[Category: Notenboom, V.]]	+	[[Category: Notenboom, V]]
-	[[Category: Rose, D R.]]	+	[[Category: Rose, D R]]
-	[[Category: Williams, S J.]]	+	[[Category: Williams, S J]]
-	[[Category: Withers, S G.]]	+	[[Category: Withers, S G]]
	[[Category: Catalytic mechanism]]		[[Category: Catalytic mechanism]]
	[[Category: Glycosyl hydrolase family 10]]		[[Category: Glycosyl hydrolase family 10]]

OCA at 11:23, 28 September 2014

OCA — Sun, 28 Sep 2014 11:23:13 GMT

←Older revision		Revision as of 11:23, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1fhd.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF THE XYLANASE CEX WITH XYLOBIOSE-DERIVED IMIDAZOLE INHIBITOR==
		+	<StructureSection load='1fhd' size='340' side='right' caption='[[1fhd]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1fhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cellulomonas_fimi Cellulomonas fimi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FHD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=XIM:5,6,7,8-TETRAHYDRO-IMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL'>XIM</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2exo\|2exo]], [[1exp\|1exp]], [[1xyl\|1xyl]], [[1fh7\|1fh7]], [[1fh8\|1fh8]], [[1fh9\|1fh9]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase Cellulose 1,4-beta-cellobiosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.91 3.2.1.91] </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=1fhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fhd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fhd RCSB], [http://www.ebi.ac.uk/pdbsum/1fhd 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/fh/1fhd_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 ==
		+	Detailed insights into the mode of binding of a series of tight-binding aza-sugar glycosidase inhibitors of two fundamentally different classes are described through X-ray crystallographic studies of complexes with the retaining family 10 xylanase Cex from Cellulomonas fimi. Complexes with xylobiose-derived aza-sugar inhibitors of the substituted "amidine" class (xylobio-imidazole, K(i) = 150 nM; xylobio-lactam oxime, K(i) = 370 nM) reveal lateral interaction of the "glycosidic" nitrogen with the acid/base catalyst (Glu127) and hydrogen bonding of the sugar 2-hydroxyl with the catalytic nucleophile (Glu233), as expected. Tight binding of xylobio-isofagomine (K(i) = 130 nM) appears to be a consequence of strong interactions of the ring nitrogen with the catalytic nucleophile while, surprisingly, no direct protein contacts are made with the ring nitrogen of the xylobio-deoxynojirimycin analogue (K(i) = 5800 nM). Instead the nitrogen interacts with two ordered water molecules, thereby accounting for its relatively weaker binding, though it still binds some 1200-fold more tightly than does xylobiose, presumably as a consequence of electrostatic interactions at the active site. Dramatically weaker binding of these same inhibitors to the family 11 xylanase Bcx from Bacillus circulans (K(i) from 0.5 to 1.5 mM) is rationalized for the substituted amidines on the basis that this enzyme utilizes a syn protonation trajectory and likely hydrolyzes via a (2,5)B boat transition state. Weaker binding of the deoxynojirimycin and isofagomine analogues likely reflects the energetic penalty for distortion of these analogues to a (2,5)B conformation, possibly coupled with destabilizing interactions with Tyr69, a conserved, catalytically essential active site residue.

-	~~{{STRUCTURE_1fhd\| PDB=1fhd \| SCENE= }}~~	+	Detailed structural analysis of glycosidase/inhibitor interactions: complexes of Cex from Cellulomonas fimi with xylobiose-derived aza-sugars.,Notenboom V, Williams SJ, Hoos R, Withers SG, Rose DR Biochemistry. 2000 Sep 26;39(38):11553-63. PMID:10995222<ref>PMID:10995222</ref>

-	~~===CRYSTAL STRUCTURE OF THE XYLANASE CEX WITH XYLOBIOSE-DERIVED IMIDAZOLE INHIBITOR===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10995222}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1fhd]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Cellulomonas_fimi Cellulomonas fimi]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010995222<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Cellulomonas fimi]]		[[Category: Cellulomonas fimi]]
	[[Category: Cellulose 1,4-beta-cellobiosidase]]		[[Category: Cellulose 1,4-beta-cellobiosidase]]

OCA: Protected "1fhd" [edit=sysop:move=sysop]

OCA — Wed, 21 Nov 2012 10:09:39 GMT

Protected "1fhd" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:09, 21 November 2012

OCA at 10:09, 21 November 2012

OCA — Wed, 21 Nov 2012 10:09:36 GMT

←Older revision		Revision as of 10:09, 21 November 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1fhd.png\|left\|200px]]		[[Image:1fhd.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1fhd", 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_1fhd\| PDB=1fhd \| SCENE= }}		{{STRUCTURE_1fhd\| PDB=1fhd \| SCENE= }}

	===CRYSTAL STRUCTURE OF THE XYLANASE CEX WITH XYLOBIOSE-DERIVED IMIDAZOLE INHIBITOR===		===CRYSTAL STRUCTURE OF THE XYLANASE CEX WITH XYLOBIOSE-DERIVED IMIDAZOLE INHIBITOR===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_10995222}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 10995222 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_10995222}}		{{ABSTRACT_PUBMED_10995222}}

	==About this Structure==		==About this Structure==
-	~~1FHD~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Cellulomonas_fimi Cellulomonas fimi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA].	+	[[1fhd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cellulomonas_fimi Cellulomonas fimi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FHD OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~10995222~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:010995222</ref><references group="xtra"/>
	[[Category: Cellulomonas fimi]]		[[Category: Cellulomonas fimi]]
	[[Category: Cellulose 1,4-beta-cellobiosidase]]		[[Category: Cellulose 1,4-beta-cellobiosidase]]
Line 33:		Line 21:
	[[Category: Catalytic mechanism]]		[[Category: Catalytic mechanism]]
	[[Category: Glycosyl hydrolase family 10]]		[[Category: Glycosyl hydrolase family 10]]
		+	[[Category: Hydrolase]]
	[[Category: Inhibitor]]		[[Category: Inhibitor]]
	[[Category: Xylanase]]		[[Category: Xylanase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:39:51 2009''