5kxe - Revision history

OCA at 11:00, 27 September 2023

OCA — Wed, 27 Sep 2023 11:00:10 GMT

←Older revision		Revision as of 11:00, 27 September 2023
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	<StructureSection load='5kxe' size='340' side='right'caption='[[5kxe]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='5kxe' size='340' side='right'caption='[[5kxe]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kxe]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Wisteria_floribunda Wisteria floribunda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KXE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KXE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kxe]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Wisteria_floribunda Wisteria floribunda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KXE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KXE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6Y2:~{N}-[(2~{S},3~{R},4~{R},5~{R},6~{R})-2-[(2~{R},3~{S},4~{R},5~{R},6~{S})-5-ACETAMIDO-2-(HYDROXYMETHYL)-6-(4-NITROPHENOXY)-4-OXIDANYL-OXAN-3-YL]OXY-6-(HYDROXYMETHYL)-4,5-BIS(OXIDANYL)OXAN-3-YL]ETHANAMIDE'>6Y2</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.09Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kxb\|5kxb]], [[5kxc\|5kxc]], [[5kxd\|5kxd]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6Y2:~{N}-[(2~{S},3~{R},4~{R},5~{R},6~{R})-2-[(2~{R},3~{S},4~{R},5~{R},6~{S})-5-ACETAMIDO-2-(HYDROXYMETHYL)-6-(4-NITROPHENOXY)-4-OXIDANYL-OXAN-3-YL]OXY-6-(HYDROXYMETHYL)-4,5-BIS(OXIDANYL)OXAN-3-YL]ETHANAMIDE'>6Y2</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></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=5kxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kxe OCA], [~~http~~://pdbe.org/5kxe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kxe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kxe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kxe 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=5kxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kxe OCA], [https://pdbe.org/5kxe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kxe RCSB], [https://www.ebi.ac.uk/pdbsum/5kxe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kxe ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1D5B395_WISFL A0A1D5B395_WISFL]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Wisteria floribunda]]		[[Category: Wisteria floribunda]]
-	[[Category: Evans~~, S V~~]]	+	[[Category: Evans SV]]
-	[[Category: Haji-Ghassemi, O]]	+	[[Category: Haji-Ghassemi O]]
-	~~[[Category: Carbohydrate-binding protein]]~~	+
-	~~[[Category: Lectin]]~~	+
-	~~[[Category: Sugar binding protein-inhibitor complex~~]]	+

OCA at 08:12, 8 January 2020

OCA — Wed, 08 Jan 2020 08:12:05 GMT

←Older revision		Revision as of 08:12, 8 January 2020
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	==Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 4.2==		==Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 4.2==
-	<StructureSection load='5kxe' size='340' side='right' caption='[[5kxe]], [[Resolution\|resolution]] 2.09Å' scene=''>	+	<StructureSection load='5kxe' size='340' side='right'caption='[[5kxe]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5kxe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Wisteria_floribunda Wisteria floribunda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KXE FirstGlance]. <br>		<table><tr><td colspan='2'>[[5kxe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Wisteria_floribunda Wisteria floribunda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KXE FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5kxe" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5kxe" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Agglutinin 3D structures\|Agglutinin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Wisteria floribunda]]		[[Category: Wisteria floribunda]]
	[[Category: Evans, S V]]		[[Category: Evans, S V]]

OCA at 18:32, 15 November 2017

OCA — Wed, 15 Nov 2017 18:32:48 GMT

←Older revision		Revision as of 18:32, 15 November 2017
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5kxe" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5kxe" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Agglutinin\|Agglutinin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:36, 21 September 2017

OCA — Thu, 21 Sep 2017 04:36:09 GMT

←Older revision		Revision as of 04:36, 21 September 2017
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5kxe" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5kxe" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Agglutinin\|Agglutinin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:25, 21 September 2016

OCA — Wed, 21 Sep 2016 06:25:18 GMT

←Older revision		Revision as of 06:25, 21 September 2016
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	<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=5kxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kxe OCA], [http://pdbe.org/5kxe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kxe RCSB], [http://www.ebi.ac.uk/pdbsum/5kxe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kxe ProSAT]</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=5kxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kxe OCA], [http://pdbe.org/5kxe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kxe RCSB], [http://www.ebi.ac.uk/pdbsum/5kxe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kxe ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aberrant glycosylation and the overexpression of specific carbohydrate epitopes is a hallmark of many cancers, and tumor-associated oligo-saccharides are actively investigated as targets for immunotherapy and diagnostics. Wisteria floribunda agglutinin (WFA) is a legume lectin that recognizes terminal N-acetylgalactosaminides with high affinity. WFA preferentially binds the disaccharide LacdiNAc (beta-D-GalNAc-[1-->4]-D-GlcNAc), which is associated with tumor malignancy in leukemia, prostate, pancreatic, ovarian, and liver cancers, and has shown promise in cancer glycobiomarker detection. The mechanism of specificity for WFA recognition of LacdiNAc is not fully understood. To address this problem, we have determined affinities and structure of WFA in complex with GalNAc and LacdiNAc. Affinities towards Gal, GalNAc, and LacdiNAc were measured via surface plasmon resonance, yielding KD values of 4.67 x 10-4 M, 9.24 x 10-5 M, and 5.45 x 10-6 M respectively. Structures of WFA in complex with LacdiNAc and GalNAc have been determined to 1.80 A - 2.32 A resolution. These high-resolution structures revealed a hydrophobic groove complementary to the GalNAc and, to a minor extent, to the backface of the GlcNAc sugar ring. Remarkably, the contribution of this small hydrophobic surface significantly increases the observed affinity for LacdiNAc over GalNAc. Tandem MS sequencing confirmed presence of two isolectin forms in commercially available WFA differing only in the identities of two amino acids. Finally, the WFA carbohydrate binding site is similar to a homologous lectin isolated from Vatairea macrocarpa in complex with GalNAc which, unlike WFA, binds not only alphaGalNAc but also terminal Ser/Thr O-linked alphaGalNAc (Tn antigen).
		+
		+	Molecular basis for recognition of the cancer glycobiomarker LacdiNAc (GalNAc(beta1-4)GlcNAc) by Wisteria floribunda agglutinin.,Haji-Ghassemi O, Gilbert M, Spence J, Schur MJ, Parker MJ, Jenkins ML, Burke JE, van Faassen H, Young NM, Evans SV J Biol Chem. 2016 Sep 6. pii: jbc.M116.750463. PMID:27601469<ref>PMID:27601469</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5kxe" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:35, 14 September 2016

OCA — Wed, 14 Sep 2016 15:35:43 GMT

←Older revision		Revision as of 15:35, 14 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5kxe is ON HOLD until Paper Publication~~	+	==Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 4.2==
-		+	<StructureSection load='5kxe' size='340' side='right' caption='[[5kxe]], [[Resolution\|resolution]] 2.09Å' scene=''>
-	~~Authors: Evans, S.V., Haji-Ghassemi, O.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5kxe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Wisteria_floribunda Wisteria floribunda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KXE FirstGlance]. <br>
-	~~Description:~~ Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 4.2	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6Y2:~{N}-[(2~{S},3~{R},4~{R},5~{R},6~{R})-2-[(2~{R},3~{S},4~{R},5~{R},6~{S})-5-ACETAMIDO-2-(HYDROXYMETHYL)-6-(4-NITROPHENOXY)-4-OXIDANYL-OXAN-3-YL]OXY-6-(HYDROXYMETHYL)-4,5-BIS(OXIDANYL)OXAN-3-YL]ETHANAMIDE'>6Y2</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kxb\|5kxb]], [[5kxc\|5kxc]], [[5kxd\|5kxd]]</td></tr>
-	[[Category: Evans, S.V]]	+	<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=5kxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kxe OCA], [http://pdbe.org/5kxe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kxe RCSB], [http://www.ebi.ac.uk/pdbsum/5kxe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kxe ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Wisteria floribunda]]
		+	[[Category: Evans, S V]]
	[[Category: Haji-Ghassemi, O]]		[[Category: Haji-Ghassemi, O]]
		+	[[Category: Carbohydrate-binding protein]]
		+	[[Category: Lectin]]
		+	[[Category: Sugar binding protein-inhibitor complex]]

OCA at 02:09, 4 August 2016

OCA — Thu, 04 Aug 2016 02:09:17 GMT

←Older revision		Revision as of 02:09, 4 August 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5kxe is ON HOLD	+	The entry 5kxe is ON HOLD until Paper Publication

	Authors: Evans, S.V., Haji-Ghassemi, O.		Authors: Evans, S.V., Haji-Ghassemi, O.

OCA: Protected "5kxe" [edit=sysop:move=sysop]

OCA — Wed, 27 Jul 2016 13:30:08 GMT

Protected "5kxe" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:30, 27 July 2016

OCA: New page: '''Unreleased structure''' The entry 5kxe is ON HOLD Authors: Evans, S.V., Haji-Ghassemi, O. Description: Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at...

OCA — Wed, 27 Jul 2016 13:30:07 GMT

New page: '''Unreleased structure''' The entry 5kxe is ON HOLD Authors: Evans, S.V., Haji-Ghassemi, O. Description: Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at...

New page

'''Unreleased structure'''

The entry 5kxe is ON HOLD

Authors: Evans, S.V., Haji-Ghassemi, O.

Description: Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 4.2
[[Category: Unreleased Structures]]
[[Category: Evans, S.V]]
[[Category: Haji-Ghassemi, O]]