1niv - Revision history

OCA at 06:08, 3 April 2024

OCA — Wed, 03 Apr 2024 06:08:54 GMT

←Older revision		Revision as of 06:08, 3 April 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1niv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NIV FirstGlance]. <br>		<table><tr><td colspan='2'>[[1niv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NIV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=~~MMA~~:O1-~~METHYL~~-MANNOSE'>~~MMA~~</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA~~-D-MANNOSE'>~~MAN~~</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]] 3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MMA:O1-METHYL-MANNOSE'>MMA</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=1niv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1niv OCA], [https://pdbe.org/1niv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1niv RCSB], [https://www.ebi.ac.uk/pdbsum/1niv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1niv 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=1niv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1niv OCA], [https://pdbe.org/1niv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1niv RCSB], [https://www.ebi.ac.uk/pdbsum/1niv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1niv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/LEC_GALNI LEC_GALNI]] Mannose-specific lectin.	+	[https://www.uniprot.org/uniprot/LEC_GALNI LEC_GALNI] Mannose-specific lectin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		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=1niv 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=1niv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Galanthus nivalis agglutinin (GNA, a 50 kDa tetramer) is a mannose-specific lectin of the Amaryllidaceae family of bulb lectins. Crystal structures of GNA complexed with methyl-alpha-D-mannose (MeMan) and mannose-alpha 1,3-D-mannose-alpha-OMe (MeMan-2) have been determined and analyzed in terms of internal structural symmetry and saccharide binding. The final model of the 2.29 A orthorhombic methyl-alpha-Man complex refined with an R-factor of 0.167 (all data) includes 12 bound sugar ligands and 327 water molecules. The four independent subunits (A, B, C and D) of the 222 tetramer and the three four-stranded beta-sheets (I,II and III) that constitute each subunit compare closely (r.m.s. delta = < 1.0 A). The 12 bound methyl-alpha-Man molecules refined with B-factors < 22 A2 and occupancies in the range of 0.5 to 1.0. The highest occupied site is located in beta-sheet I (site 1), where interactions from the dimer-related subunit contribute to complex stabilization. These subunit pairs (A-D and B-C) associate tightly with a buried surface area of 1738 A2 and 33 interchain hydrogen bonds resulting from C-terminal strand exchange. In comparison, the A-B and C-D subunit pairs have narrow interfaces (476 A2) and no direct H-bond contacts. The 3.0 A structure of the cubic Man-alpha 1,3-Man-OMe complex, determined by molecular replacement and refined with X-PLOR using NCS constraints and density modification methods, is less well ordered due to a high crystal solvent content (68%). Complexed disaccharide is responsible for the most crucial lattice contacts, which involve only one of the two independent subunits (A). The second subunit (C) shows a high degree of flexibility (Bav = 41.7 A2). The complete disaccharide molecule is visible in both subunits at site 3, which is the only extended site. The ligand is oriented with its reducing end positioned in the specificity pocket. The non-reducing manose is in contact through hydrogen bonding with a charged subsite (D37-K38) on the 2-fold-related subunit (A-B or C-D interfaces). Bound Man-alpha 1,3-MeMan is also well defined in site 2 of subunit A, as a result of favorable lattice contacts, while only the mannose residue bound in the specificity pocket is visible at site 2 of subunit C and site 1 of both subunits. Together these results suggest that strong binding correlates with the presence of subsidiary contacts coming either from a dimer-related subunit or from lattice interactions. Site 1 is most specific for terminal non-reducing or reducing mannose, while site 3 is extended and complementary to alpha-1,3 linked mannose oligosaccharides.
-
-	The mannose-specific bulb lectin from Galanthus nivalis (snowdrop) binds mono- and dimannosides at distinct sites. Structure analysis of refined complexes at 2.3 A and 3.0 A resolution.,Hester G, Wright CS J Mol Biol. 1996 Oct 4;262(4):516-31. PMID:8893860<ref>PMID:8893860</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1niv" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Agglutinin 3D structures\|Agglutinin 3D structures]]		*[[Agglutinin 3D structures\|Agglutinin 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Galanthus nivalis]]		[[Category: Galanthus nivalis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hester, G]]	+	[[Category: Hester G]]
-	[[Category: Wright~~, C S]]~~	+	[[Category: Wright CS]]
-	~~[[Category: Lectin]]~~	+
-	~~[[Category: Mannose-binding~~]]	+

OCA at 09:35, 5 May 2021

OCA — Wed, 05 May 2021 09:35:15 GMT

←Older revision		Revision as of 09:35, 5 May 2021
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	<StructureSection load='1niv' size='340' side='right'caption='[[1niv]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1niv' size='340' side='right'caption='[[1niv]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1niv]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1NIV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1niv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NIV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MDM~~:METHYL~~-O3-(ALPHA-D~~-MANNOSE)-ALPHA-D-MANNOSE'>~~MDM~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MMA:O1-METHYL-MANNOSE'>MMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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=1niv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1niv OCA], [~~http~~://pdbe.org/1niv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1niv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1niv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1niv 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=1niv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1niv OCA], [https://pdbe.org/1niv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1niv RCSB], [https://www.ebi.ac.uk/pdbsum/1niv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1niv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/LEC_GALNI LEC_GALNI]] Mannose-specific lectin.	+	[[https://www.uniprot.org/uniprot/LEC_GALNI LEC_GALNI]] Mannose-specific lectin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:01, 31 July 2019

OCA — Wed, 31 Jul 2019 08:01:51 GMT

←Older revision		Revision as of 08:01, 31 July 2019
Line 1:		Line 1:

	==MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA 1,3-METHYL-D-MANNOSE==		==MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA 1,3-METHYL-D-MANNOSE==
-	<StructureSection load='1niv' size='340' side='right' caption='[[1niv]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='1niv' size='340' side='right'caption='[[1niv]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1niv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NIV FirstGlance]. <br>		<table><tr><td colspan='2'>[[1niv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NIV FirstGlance]. <br>
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/ni/1niv_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ni/1niv_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>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1niv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1niv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Agglutinin 3D structures\|Agglutinin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Galanthus nivalis]]		[[Category: Galanthus nivalis]]
		+	[[Category: Large Structures]]
	[[Category: Hester, G]]		[[Category: Hester, G]]
	[[Category: Wright, C S]]		[[Category: Wright, C S]]
	[[Category: Lectin]]		[[Category: Lectin]]
	[[Category: Mannose-binding]]		[[Category: Mannose-binding]]

OCA at 10:22, 25 October 2017

OCA — Wed, 25 Oct 2017 10:22:55 GMT

←Older revision		Revision as of 10:22, 25 October 2017
Line 1:		Line 1:
		+
	==MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA 1,3-METHYL-D-MANNOSE==		==MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA 1,3-METHYL-D-MANNOSE==
	<StructureSection load='1niv' size='340' side='right' caption='[[1niv]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1niv' size='340' side='right' caption='[[1niv]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1niv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NIV FirstGlance]. <br>		<table><tr><td colspan='2'>[[1niv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NIV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MDM:METHYL-O3-(ALPHA-D-MANNOSE)-ALPHA-D-MANNOSE'>MDM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MDM:METHYL-O3-(ALPHA-D-MANNOSE)-ALPHA-D-MANNOSE'>MDM</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=1niv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1niv OCA], [http://pdbe.org/1niv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1niv RCSB], [http://www.ebi.ac.uk/pdbsum/1niv 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=1niv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1niv OCA], [http://pdbe.org/1niv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1niv RCSB], [http://www.ebi.ac.uk/pdbsum/1niv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1niv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		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=1niv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:19, 11 September 2015

OCA — Fri, 11 Sep 2015 10:19:30 GMT

←Older revision		Revision as of 10:19, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1niv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NIV FirstGlance]. <br>		<table><tr><td colspan='2'>[[1niv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NIV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MDM:METHYL-O3-(ALPHA-D-MANNOSE)-ALPHA-D-MANNOSE'>MDM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MDM:METHYL-O3-(ALPHA-D-MANNOSE)-ALPHA-D-MANNOSE'>MDM</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=1niv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1niv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1niv RCSB], [http://www.ebi.ac.uk/pdbsum/1niv 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=1niv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1niv OCA], [http://pdbe.org/1niv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1niv RCSB], [http://www.ebi.ac.uk/pdbsum/1niv PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	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 1niv" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:06, 25 December 2014

OCA — Thu, 25 Dec 2014 15:06:01 GMT

←Older revision		Revision as of 15:06, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1niv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NIV FirstGlance]. <br>		<table><tr><td colspan='2'>[[1niv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NIV FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MDM:METHYL-O3-(ALPHA-D-MANNOSE)-ALPHA-D-MANNOSE'>MDM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MDM:METHYL-O3-(ALPHA-D-MANNOSE)-ALPHA-D-MANNOSE'>MDM</scene></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=1niv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1niv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1niv RCSB], [http://www.ebi.ac.uk/pdbsum/1niv 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=1niv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1niv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1niv RCSB], [http://www.ebi.ac.uk/pdbsum/1niv PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LEC_GALNI LEC_GALNI]] Mannose-specific lectin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Galanthus nivalis]]		[[Category: Galanthus nivalis]]
-	[[Category: Hester, G.]]	+	[[Category: Hester, G]]
-	[[Category: Wright, C S.]]	+	[[Category: Wright, C S]]
	[[Category: Lectin]]		[[Category: Lectin]]
	[[Category: Mannose-binding]]		[[Category: Mannose-binding]]

OCA at 18:42, 28 September 2014

OCA — Sun, 28 Sep 2014 18:42:53 GMT

←Older revision		Revision as of 18:42, 28 September 2014
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-	[[~~Image~~:1niv.~~png\|left~~\|200px]]	+	==MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA 1,3-METHYL-D-MANNOSE==
		+	<StructureSection load='1niv' size='340' side='right' caption='[[1niv]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1niv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NIV FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MDM:METHYL-O3-(ALPHA-D-MANNOSE)-ALPHA-D-MANNOSE'>MDM</scene><br>
		+	<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=1niv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1niv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1niv RCSB], [http://www.ebi.ac.uk/pdbsum/1niv 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/ni/1niv_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 ==
		+	Galanthus nivalis agglutinin (GNA, a 50 kDa tetramer) is a mannose-specific lectin of the Amaryllidaceae family of bulb lectins. Crystal structures of GNA complexed with methyl-alpha-D-mannose (MeMan) and mannose-alpha 1,3-D-mannose-alpha-OMe (MeMan-2) have been determined and analyzed in terms of internal structural symmetry and saccharide binding. The final model of the 2.29 A orthorhombic methyl-alpha-Man complex refined with an R-factor of 0.167 (all data) includes 12 bound sugar ligands and 327 water molecules. The four independent subunits (A, B, C and D) of the 222 tetramer and the three four-stranded beta-sheets (I,II and III) that constitute each subunit compare closely (r.m.s. delta = < 1.0 A). The 12 bound methyl-alpha-Man molecules refined with B-factors < 22 A2 and occupancies in the range of 0.5 to 1.0. The highest occupied site is located in beta-sheet I (site 1), where interactions from the dimer-related subunit contribute to complex stabilization. These subunit pairs (A-D and B-C) associate tightly with a buried surface area of 1738 A2 and 33 interchain hydrogen bonds resulting from C-terminal strand exchange. In comparison, the A-B and C-D subunit pairs have narrow interfaces (476 A2) and no direct H-bond contacts. The 3.0 A structure of the cubic Man-alpha 1,3-Man-OMe complex, determined by molecular replacement and refined with X-PLOR using NCS constraints and density modification methods, is less well ordered due to a high crystal solvent content (68%). Complexed disaccharide is responsible for the most crucial lattice contacts, which involve only one of the two independent subunits (A). The second subunit (C) shows a high degree of flexibility (Bav = 41.7 A2). The complete disaccharide molecule is visible in both subunits at site 3, which is the only extended site. The ligand is oriented with its reducing end positioned in the specificity pocket. The non-reducing manose is in contact through hydrogen bonding with a charged subsite (D37-K38) on the 2-fold-related subunit (A-B or C-D interfaces). Bound Man-alpha 1,3-MeMan is also well defined in site 2 of subunit A, as a result of favorable lattice contacts, while only the mannose residue bound in the specificity pocket is visible at site 2 of subunit C and site 1 of both subunits. Together these results suggest that strong binding correlates with the presence of subsidiary contacts coming either from a dimer-related subunit or from lattice interactions. Site 1 is most specific for terminal non-reducing or reducing mannose, while site 3 is extended and complementary to alpha-1,3 linked mannose oligosaccharides.

-	~~{{STRUCTURE_1niv\| PDB=1niv \| SCENE= }}~~	+	The mannose-specific bulb lectin from Galanthus nivalis (snowdrop) binds mono- and dimannosides at distinct sites. Structure analysis of refined complexes at 2.3 A and 3.0 A resolution.,Hester G, Wright CS J Mol Biol. 1996 Oct 4;262(4):516-31. PMID:8893860<ref>PMID:8893860</ref>

-	~~===MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA 1~~,~~3-METHYL-D-MANNOSE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8893860}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1niv]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Galanthus_nivalis Galanthus nivalis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:008893860<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Galanthus nivalis]]		[[Category: Galanthus nivalis]]
	[[Category: Hester, G.]]		[[Category: Hester, G.]]

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

OCA — Wed, 05 Dec 2012 21:27:08 GMT

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

←Older revision

Revision as of 21:27, 5 December 2012

OCA at 21:27, 5 December 2012

OCA — Wed, 05 Dec 2012 21:27:05 GMT

←Older revision		Revision as of 21:27, 5 December 2012
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-	{{Seed}}
	[[Image:1niv.png\|left\|200px]]		[[Image:1niv.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1niv", 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.
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	{{STRUCTURE_1niv\| PDB=1niv \| SCENE= }}		{{STRUCTURE_1niv\| PDB=1niv \| SCENE= }}

	===MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA 1,3-METHYL-D-MANNOSE===		===MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA 1,3-METHYL-D-MANNOSE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_8893860}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 8893860 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_8893860}}		{{ABSTRACT_PUBMED_8893860}}

	==About this Structure==		==About this Structure==
-	~~1NIV~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA].	+	[[1niv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~8893860~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:008893860</ref><references group="xtra"/>
	[[Category: Galanthus nivalis]]		[[Category: Galanthus nivalis]]
	[[Category: Hester, G.]]		[[Category: Hester, G.]]
Line 29:		Line 17:
	[[Category: Lectin]]		[[Category: Lectin]]
	[[Category: Mannose-binding]]		[[Category: Mannose-binding]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 19:45:31 2009''

OCA at 17:45, 17 February 2009

OCA — Tue, 17 Feb 2009 17:45:31 GMT

←Older revision		Revision as of 17:45, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1NIV is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA].	+	1NIV is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Galanthus_nivalis Galanthus nivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NIV OCA].

	==Reference==		==Reference==
-	The mannose-specific bulb lectin from Galanthus nivalis (snowdrop) binds mono- and dimannosides at distinct sites. Structure analysis of refined complexes at 2.3 A and 3.0 A resolution., Hester G, Wright CS, J Mol Biol. 1996 Oct 4;262(4):516-31. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/8893860 8893860]~~	+	<ref group="xtra">PMID:8893860</ref><references group="xtra"/>
	[[Category: Galanthus nivalis]]		[[Category: Galanthus nivalis]]
-	[[Category: Single protein]]
	[[Category: Hester, G.]]		[[Category: Hester, G.]]
	[[Category: Wright, C S.]]		[[Category: Wright, C S.]]
Line 31:		Line 30:
	[[Category: Mannose-binding]]		[[Category: Mannose-binding]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 03~~:39:~~02 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 19:45:31 2009''