6i77 - Revision history

OCA at 11:48, 24 January 2024

OCA — Wed, 24 Jan 2024 11:48:21 GMT

←Older revision		Revision as of 11:48, 24 January 2024
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	==Galectin-3C in complex with substituted polyfluoroaryl monothiogalactoside derivative-4==		==Galectin-3C in complex with substituted polyfluoroaryl monothiogalactoside derivative-4==
-	<StructureSection load='6i77' size='340' side='right' caption='[[6i77]], [[Resolution\|resolution]] 1.22Å' scene=''>	+	<StructureSection load='6i77' size='340' side='right'caption='[[6i77]], [[Resolution\|resolution]] 1.22Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i77]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I77 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6I77 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i77]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I77 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I77 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H5Q:(2~{R},3~{R},4~{S},5~{R},6~{S})-4-[4-[4-azanyl-2,3,5,6-tetrakis(fluoranyl)phenyl]-1,2,3-triazol-1-yl]-2-(hydroxymethyl)-6-(4-methylphenyl)sulfanyl-oxane-3,5-diol'>H5Q</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]] 1.219Å</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=6i77 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i77 OCA], [~~http~~://pdbe.org/6i77 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6i77 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6i77 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6i77 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H5Q:(2~{R},3~{R},4~{S},5~{R},6~{S})-4-[4-[4-azanyl-2,3,5,6-tetrakis(fluoranyl)phenyl]-1,2,3-triazol-1-yl]-2-(hydroxymethyl)-6-(4-methylphenyl)sulfanyl-oxane-3,5-diol'>H5Q</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=6i77 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i77 OCA], [https://pdbe.org/6i77 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i77 RCSB], [https://www.ebi.ac.uk/pdbsum/6i77 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i77 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LEG3_HUMAN LEG3_HUMAN]] Galactose-specific lectin which binds IgE. May mediate with the alpha-3, beta-1 integrin the stimulation by CSPG4 of endothelial cells migration. Together with DMBT1, required for terminal differentiation of columnar epithelial cells during early embryogenesis (By similarity). In the nucleus: acts as a pre-mRNA splicing factor. Involved in acute inflammatory responses including neutrophil activation and adhesion, chemoattraction of monocytes macrophages, opsonization of apoptotic neutrophils, and activation of mast cells.<ref>PMID:15181153</ref> <ref>PMID:19594635</ref> <ref>PMID:19616076</ref>	+	[https://www.uniprot.org/uniprot/LEG3_HUMAN LEG3_HUMAN] Galactose-specific lectin which binds IgE. May mediate with the alpha-3, beta-1 integrin the stimulation by CSPG4 of endothelial cells migration. Together with DMBT1, required for terminal differentiation of columnar epithelial cells during early embryogenesis (By similarity). In the nucleus: acts as a pre-mRNA splicing factor. Involved in acute inflammatory responses including neutrophil activation and adhesion, chemoattraction of monocytes macrophages, opsonization of apoptotic neutrophils, and activation of mast cells.<ref>PMID:15181153</ref> <ref>PMID:19594635</ref> <ref>PMID:19616076</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6i77" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6i77" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Galectin 3D structures\|Galectin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Kumar, R~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Logan, D T~~]]	+	[[Category: Kumar R]]
-	[[Category: ~~Nilsson, U J~~]]	+	[[Category: Logan DT]]
-	[[Category: ~~Peterson, K~~]]	+	[[Category: Nilsson UJ]]
-	[[Category: ~~Carbohydrate-binding protein]]~~	+	[[Category: Peterson K]]
-	~~[[Category: Galactose-specific lectin 3]]~~	+
-	~~[[Category: Galactoside-binding protein]]~~	+
-	~~[[Category: Galbp]]~~	+
-	~~[[Category: Ige-6 binding protein]]~~	+
-	~~[[Category: L-31]]~~	+
-	~~[[Category: Laminin-binding protein]]~~	+
-	~~[[Category: Lectin]]~~	+
-	~~[[Category: Lectin l-29]]~~	+
-	~~[[Category: Mac-2]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 09:52, 13 February 2019

OCA — Wed, 13 Feb 2019 09:52:55 GMT

←Older revision		Revision as of 09:52, 13 February 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6i77 is ~~ON HOLD~~	+	==Galectin-3C in complex with substituted polyfluoroaryl monothiogalactoside derivative-4==
		+	<StructureSection load='6i77' size='340' side='right' caption='[[6i77]], [[Resolution\|resolution]] 1.22Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6i77]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I77 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I77 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H5Q:(2~{R},3~{R},4~{S},5~{R},6~{S})-4-[4-[4-azanyl-2,3,5,6-tetrakis(fluoranyl)phenyl]-1,2,3-triazol-1-yl]-2-(hydroxymethyl)-6-(4-methylphenyl)sulfanyl-oxane-3,5-diol'>H5Q</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=6i77 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i77 OCA], [http://pdbe.org/6i77 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i77 RCSB], [http://www.ebi.ac.uk/pdbsum/6i77 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i77 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LEG3_HUMAN LEG3_HUMAN]] Galactose-specific lectin which binds IgE. May mediate with the alpha-3, beta-1 integrin the stimulation by CSPG4 of endothelial cells migration. Together with DMBT1, required for terminal differentiation of columnar epithelial cells during early embryogenesis (By similarity). In the nucleus: acts as a pre-mRNA splicing factor. Involved in acute inflammatory responses including neutrophil activation and adhesion, chemoattraction of monocytes macrophages, opsonization of apoptotic neutrophils, and activation of mast cells.<ref>PMID:15181153</ref> <ref>PMID:19594635</ref> <ref>PMID:19616076</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In the beta-d-galactopyranoside-binding protein galectin-3, synthetic inhibitors substituted at the 3-position of a thiodigalactoside core cause the formation of an aglycone binding pocket through the displacement of an arginine residue (Arg144) from its position in the apoprotein. To examine in detail the role of different molecular interactions in this pocket, we have synthesized a series of nine 3-(4-(2,3,5,6-tetrafluorophenyl)-1,2,3-triazol-1-yl)-thiogalactosides with different para substituents and measured their affinities to galectin-3 using a fluorescence polarization assay. High-resolution crystal structures (<1.3 A) have been determined for five of the ligands in complex with the C-terminal domain of galectin-3. The binding affinities are rationalised with the help of the three-dimensional structures and quantum-mechanical calculations. Three effects seem to be involved: Firstly, the binding pocket is too small for the largest ligands with ethyl and methyl. Secondly, for the other ligands, the affinity seems to be determined mainly by desolvation effects, disfavouring the polar substituents, but this is partly counteracted by the cation-pi interaction with Arg144, which stacks on top of the substituted tetrafluorophenyl group in all complexes. The results provide detailed insight into interactions of fluorinated phenyl moieties with arginine-containing protein binding sites and the complex interplay of different energetic components in defining the binding affinity.

-	~~Authors: Kumar~~, R., ~~Peterson~~, K., ~~Nilsson~~, U~~.J.~~, ~~Logan~~, D.T.	+	Substituted polyfluoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation effects.,Kumar R, Peterson K, Misini Ignjatovic M, Leffler H, Ryde U, Nilsson UJ, Logan DT Org Biomol Chem. 2019 Jan 31;17(5):1081-1089. doi: 10.1039/c8ob02888e. PMID:30632578<ref>PMID:30632578</ref>

-	~~Description: Galectin~~-~~3C in complex with substituted polyfluoroaryl monothiogalactoside derivative~~-4	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Logan, D.T~~]]	+	<div class="pdbe-citations 6i77" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
	[[Category: Kumar, R]]		[[Category: Kumar, R]]
		+	[[Category: Logan, D T]]
		+	[[Category: Nilsson, U J]]
	[[Category: Peterson, K]]		[[Category: Peterson, K]]
-	[[Category: ~~Nilsson, U.J~~]]	+	[[Category: Carbohydrate-binding protein]]
		+	[[Category: Galactose-specific lectin 3]]
		+	[[Category: Galactoside-binding protein]]
		+	[[Category: Galbp]]
		+	[[Category: Ige-6 binding protein]]
		+	[[Category: L-31]]
		+	[[Category: Laminin-binding protein]]
		+	[[Category: Lectin]]
		+	[[Category: Lectin l-29]]
		+	[[Category: Mac-2]]
		+	[[Category: Sugar binding protein]]

OCA: Protected "6i77" [edit=sysop:move=sysop]

OCA — Sun, 02 Dec 2018 18:40:51 GMT

Protected "6i77" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:40, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6i77 is ON HOLD Authors: Kumar, R., Peterson, K., Nilsson, U.J., Logan, D.T. Description: Galectin-3C in complex with substituted polyfluoroaryl mo...

OCA — Sun, 02 Dec 2018 18:40:49 GMT

New page: '''Unreleased structure''' The entry 6i77 is ON HOLD Authors: Kumar, R., Peterson, K., Nilsson, U.J., Logan, D.T. Description: Galectin-3C in complex with substituted polyfluoroaryl mo...

New page

'''Unreleased structure'''

The entry 6i77 is ON HOLD

Authors: Kumar, R., Peterson, K., Nilsson, U.J., Logan, D.T.

Description: Galectin-3C in complex with substituted polyfluoroaryl monothiogalactoside derivative-4
[[Category: Unreleased Structures]]
[[Category: Logan, D.T]]
[[Category: Kumar, R]]
[[Category: Peterson, K]]
[[Category: Nilsson, U.J]]