5tg3 - Revision history

OCA at 13:00, 4 October 2023

2023-10-04T13:00:03Z

←Older revision		Revision as of 13:00, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5tg3' size='340' side='right'caption='[[5tg3]], [[Resolution\|resolution]] 1.77Å' scene=''>		<StructureSection load='5tg3' size='340' side='right'caption='[[5tg3]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tg3]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Dioclea_reflexa Dioclea reflexa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TG3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5TG3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tg3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Macropsychanthus_comosus Macropsychanthus comosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TG3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TG3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</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]] 1.765Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5tg3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tg3 OCA], [~~http~~://pdbe.org/5tg3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tg3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tg3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tg3 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</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=5tg3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tg3 OCA], [https://pdbe.org/5tg3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tg3 RCSB], [https://www.ebi.ac.uk/pdbsum/5tg3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tg3 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/LECA_DIORF LECA_DIORF]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Dioclea reflexa]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Araripe~~, D A~~]]	+	[[Category: Macropsychanthus comosus]]
-	[[Category: Cavada~~, B S~~]]	+	[[Category: Araripe DA]]
-	[[Category: Correia~~, J L.A~~]]	+	[[Category: Cavada BS]]
-	[[Category: Delatorre, P]]	+	[[Category: Correia JLA]]
-	[[Category: Lossio~~, C F~~]]	+	[[Category: Delatorre P]]
-	[[Category: Nascimento~~, K S~~]]	+	[[Category: Lossio CF]]
-	[[Category: Neco~~, A H.B~~]]	+	[[Category: Nascimento KS]]
-	[[Category: Osterne~~, V J.S~~]]	+	[[Category: Neco AHB]]
-	[[Category: Pereira~~, R I~~]]	+	[[Category: Osterne VJS]]
-	[[Category: Pinto-Junior~~, V R~~]]	+	[[Category: Pereira RI]]
-	[[Category: Rocha~~, B A.M~~]]	+	[[Category: Pinto-Junior VR]]
-	[[Category: Santiago~~, M Q~~]]	+	[[Category: Rocha BAM]]
-	[[Category: Silva-Filho~~, J C]]~~	+	[[Category: Santiago MQ]]
-	~~[[Category: Drfl]]~~	+	[[Category: Silva-Filho JC]]
-	~~[[Category: Lectin]]~~	+
-	~~[[Category: Sugar binding protein]]~~	+
-	~~[[Category: X-man~~]]	+

OCA at 12:09, 23 September 2020

2020-09-23T12:09:34Z

←Older revision		Revision as of 12:09, 23 September 2020
Line 1:		Line 1:

	==Crystal Structure of Dioclea reflexa seed lectin (DrfL) in complex with X-Man==		==Crystal Structure of Dioclea reflexa seed lectin (DrfL) in complex with X-Man==
-	<StructureSection load='5tg3' size='340' side='right' caption='[[5tg3]], [[Resolution\|resolution]] 1.77Å' scene=''>	+	<StructureSection load='5tg3' size='340' side='right'caption='[[5tg3]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tg3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Dioclea_reflexa Dioclea reflexa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TG3 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TG3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tg3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Dioclea_reflexa Dioclea reflexa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TG3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5TG3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</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=5tg3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tg3 OCA], [http://pdbe.org/5tg3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tg3 RCSB], [http://www.ebi.ac.uk/pdbsum/5tg3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tg3 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5tg3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tg3 OCA], [http://pdbe.org/5tg3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tg3 RCSB], [http://www.ebi.ac.uk/pdbsum/5tg3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tg3 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Dioclea reflexa]]		[[Category: Dioclea reflexa]]
		+	[[Category: Large Structures]]
	[[Category: Araripe, D A]]		[[Category: Araripe, D A]]
	[[Category: Cavada, B S]]		[[Category: Cavada, B S]]

OCA at 17:45, 10 March 2017

2017-03-10T17:45:24Z

←Older revision		Revision as of 17:45, 10 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tg3 is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Dioclea reflexa seed lectin (DrfL) in complex with X-Man==
		+	<StructureSection load='5tg3' size='340' side='right' caption='[[5tg3]], [[Resolution\|resolution]] 1.77Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5tg3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Dioclea_reflexa Dioclea reflexa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TG3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TG3 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=XMM:(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>XMM</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=5tg3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tg3 OCA], [http://pdbe.org/5tg3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tg3 RCSB], [http://www.ebi.ac.uk/pdbsum/5tg3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tg3 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The three-dimensional structure of Dioclea reflexa seed lectin (DrfL) was studied in detail by a combination of X-ray crystallography, molecular docking and molecular dynamics. DrfL was purified by affinity chromatography using Sephadex G-50 matrix. Its primary structure was obtained by mass spectrometry, and crystals belonging to orthorhombic space group P212121 were grown by the vapor diffusion method at 293K. The crystal structure was solved at 1.765A and was very similar to that of other lectins from the same subtribe. The structure presented Rfactor and Rfree of 21.69% and 24.89%, respectively, with no residues in nonallowed regions of Ramachandran plot. Similar to other Diocleinae lectins, DrfL was capable of relaxing aortic rings via NO induction, with CRD participation, albeit with low intensity (32%). In silico analysis results demonstrated that DrfL could strongly interact with complex N-glycans, components of blood vessel glycoconjugates. Despite the high similarity among Diocleinae lectins, it was also reported that each lectin has unique CRD properties that influence carbohydrate binding, resulting in different biological effects presented by these molecules.

-	~~Authors~~: ~~Santiago~~, ~~M.Q., Correia, J.L.A~~., Pinto-Junior~~, V.R.~~, Osterne, ~~V.J.S.~~, Pereira, ~~R.I.~~, Silva-Filho, ~~J.C., Lossio, C.F.~~, Rocha, ~~B.A.M.~~, ~~Delatorre~~, P.~~, Neco, A~~.H.B.~~, Araripe, D~~.A.~~, Nascimento, K~~.~~S., Cavada, B.S~~.	+	Structural studies of a vasorelaxant lectin from Dioclea reflexa Hook seeds: Crystal structure, molecular docking and dynamics.,Pinto-Junior VR, Osterne VJ, Santiago MQ, Correia JL, Pereira-Junior FN, Leal RB, Pereira MG, Chicas LS, Nagano CS, Rocha BA, Silva-Filho JC, Ferreira WP, Rocha CR, Nascimento KS, Assreuy AM, Cavada BS Int J Biol Macromol. 2017 Jan 24;98:12-23. doi: 10.1016/j.ijbiomac.2017.01.092. PMID:28130130<ref>PMID:28130130</ref>

-	~~Description: Crystal Structure~~ of ~~Dioclea reflexa seed lectin (DrfL) in complex with X-Man~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Lossio, C~~.~~F]]~~	+	<div class="pdbe-citations 5tg3" style="background-color:#fffaf0;"></div>
-	~~[[Category: Rocha, B~~.A.~~M]]~~	+	== References ==
-	~~[[Category: Correia, J.L.A]]~~	+	<references/>
-	~~[[Category~~: ~~Nascimento, K.S]]~~	+	__TOC__
-	~~[[Category: Silva-Filho, J.C]]~~	+	</StructureSection>
-	~~[[Category: Neco, A.H.B]]~~	+	[[Category: Dioclea reflexa]]
-	~~[[Category: Pinto-Junior, V.R]]~~	+	[[Category: Araripe, D A]]
-	[[Category: ~~Pereira, R.I~~]]	+	[[Category: Cavada, B S]]
-	[[Category: ~~Santiago~~, ~~M.Q~~]]	+	[[Category: Correia, J L.A]]
-	[[Category: ~~Osterne~~, ~~V.J.~~S]]	+
-	[[Category: ~~Cavada~~, B.S]]	+
	[[Category: Delatorre, P]]		[[Category: Delatorre, P]]
-	[[Category: ~~Araripe~~, D.A]]	+	[[Category: Lossio, C F]]
		+	[[Category: Nascimento, K S]]
		+	[[Category: Neco, A H.B]]
		+	[[Category: Osterne, V J.S]]
		+	[[Category: Pereira, R I]]
		+	[[Category: Pinto-Junior, V R]]
		+	[[Category: Rocha, B A.M]]
		+	[[Category: Santiago, M Q]]
		+	[[Category: Silva-Filho, J C]]
		+	[[Category: Drfl]]
		+	[[Category: Lectin]]
		+	[[Category: Sugar binding protein]]
		+	[[Category: X-man]]

OCA at 14:46, 4 January 2017

2017-01-04T14:46:43Z

←Older revision		Revision as of 14:46, 4 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5tg3 is ON HOLD	+	The entry 5tg3 is ON HOLD until Paper Publication

	Authors: Santiago, M.Q., Correia, J.L.A., Pinto-Junior, V.R., Osterne, V.J.S., Pereira, R.I., Silva-Filho, J.C., Lossio, C.F., Rocha, B.A.M., Delatorre, P., Neco, A.H.B., Araripe, D.A., Nascimento, K.S., Cavada, B.S.		Authors: Santiago, M.Q., Correia, J.L.A., Pinto-Junior, V.R., Osterne, V.J.S., Pereira, R.I., Silva-Filho, J.C., Lossio, C.F., Rocha, B.A.M., Delatorre, P., Neco, A.H.B., Araripe, D.A., Nascimento, K.S., Cavada, B.S.

OCA: Protected "5tg3" [edit=sysop:move=sysop]

2016-10-05T20:02:22Z

Protected "5tg3" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:02, 5 October 2016

OCA: New page: '''Unreleased structure''' The entry 5tg3 is ON HOLD Authors: Santiago, M.Q., Correia, J.L.A., Pinto-Junior, V.R., Osterne, V.J.S., Pereira, R.I., Silva-Filho, J.C., Lossio, C.F., Rocha...

2016-10-05T20:02:20Z

New page: '''Unreleased structure''' The entry 5tg3 is ON HOLD Authors: Santiago, M.Q., Correia, J.L.A., Pinto-Junior, V.R., Osterne, V.J.S., Pereira, R.I., Silva-Filho, J.C., Lossio, C.F., Rocha...

New page

'''Unreleased structure'''

The entry 5tg3 is ON HOLD

Authors: Santiago, M.Q., Correia, J.L.A., Pinto-Junior, V.R., Osterne, V.J.S., Pereira, R.I., Silva-Filho, J.C., Lossio, C.F., Rocha, B.A.M., Delatorre, P., Neco, A.H.B., Araripe, D.A., Nascimento, K.S., Cavada, B.S.

Description: Crystal Structure of Dioclea reflexa seed lectin (DrfL) in complex with X-Man
[[Category: Unreleased Structures]]
[[Category: Lossio, C.F]]
[[Category: Rocha, B.A.M]]
[[Category: Correia, J.L.A]]
[[Category: Nascimento, K.S]]
[[Category: Silva-Filho, J.C]]
[[Category: Neco, A.H.B]]
[[Category: Pinto-Junior, V.R]]
[[Category: Pereira, R.I]]
[[Category: Santiago, M.Q]]
[[Category: Osterne, V.J.S]]
[[Category: Cavada, B.S]]
[[Category: Delatorre, P]]
[[Category: Araripe, D.A]]