5t7p - Revision history

OCA at 12:56, 4 October 2023

OCA — Wed, 04 Oct 2023 12:56:06 GMT

←Older revision		Revision as of 12:56, 4 October 2023
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	<StructureSection load='5t7p' size='340' side='right'caption='[[5t7p]], [[Resolution\|resolution]] 2.16Å' scene=''>		<StructureSection load='5t7p' size='340' side='right'caption='[[5t7p]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t7p]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pisum_sativum Pisum sativum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T7P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5T7P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t7p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pisum_sativum Pisum sativum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T7P 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]] 2.16Å</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=5t7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t7p OCA], [~~http~~://pdbe.org/5t7p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5t7p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5t7p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5t7p 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=5t7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t7p OCA], [https://pdbe.org/5t7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t7p RCSB], [https://www.ebi.ac.uk/pdbsum/5t7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t7p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/LEC_PEA LEC_PEA]] D-mannose specific lectin.	+	[https://www.uniprot.org/uniprot/LEC_PEA LEC_PEA] D-mannose specific lectin.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 25:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Pisum sativum]]		[[Category: Pisum sativum]]
-	[[Category: Cavada~~, B S~~]]	+	[[Category: Cavada BS]]
-	[[Category: Delatorre, P]]	+	[[Category: Delatorre P]]
-	[[Category: Nascimento~~, K S~~]]	+	[[Category: Nascimento KS]]
-	[[Category: Osterne~~, V J.S~~]]	+	[[Category: Osterne VJS]]
-	[[Category: Pinto-Junior~~, V R~~]]	+	[[Category: Pinto-Junior VR]]
-	[[Category: Rocha~~, B A.M~~]]	+	[[Category: Rocha BAM]]
-	[[Category: Santiago~~, M Q~~]]	+	[[Category: Santiago MQ]]
-	[[Category: Silva-Filho~~, J C]]~~	+	[[Category: Silva-Filho JC]]
-	~~[[Category: Lectin]]~~	+
-	~~[[Category: Pal]]~~	+
-	~~[[Category: Pisum arvense]]~~	+
-	~~[[Category: Sugar binding protein]]~~	+
-	~~[[Category: X-man~~]]	+

OCA at 11:25, 16 September 2020

OCA — Wed, 16 Sep 2020 11:25:06 GMT

←Older revision		Revision as of 11:25, 16 September 2020
Line 1:		Line 1:

	==Crystal structure of Pisum arvense lectin (PAL) complexed with X-Man==		==Crystal structure of Pisum arvense lectin (PAL) complexed with X-Man==
-	<StructureSection load='5t7p' size='340' side='right' caption='[[5t7p]], [[Resolution\|resolution]] 2.16Å' scene=''>	+	<StructureSection load='5t7p' size='340' side='right'caption='[[5t7p]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t7p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pisum_sativum Pisum sativum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T7P OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5T7P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t7p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pisum_sativum Pisum sativum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T7P OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5T7P 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=5t7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t7p OCA], [http://pdbe.org/5t7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t7p RCSB], [http://www.ebi.ac.uk/pdbsum/5t7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t7p 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=5t7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t7p OCA], [http://pdbe.org/5t7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t7p RCSB], [http://www.ebi.ac.uk/pdbsum/5t7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t7p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pisum sativum]]		[[Category: Pisum sativum]]
	[[Category: Cavada, B S]]		[[Category: Cavada, B S]]

OCA at 09:01, 9 August 2017

OCA — Wed, 09 Aug 2017 09:01:56 GMT

←Older revision		Revision as of 09:01, 9 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5t7p is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Pisum arvense lectin (PAL) complexed with X-Man==
		+	<StructureSection load='5t7p' size='340' side='right' caption='[[5t7p]], [[Resolution\|resolution]] 2.16Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5t7p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pisum_sativum Pisum sativum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T7P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T7P 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=5t7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t7p OCA], [http://pdbe.org/5t7p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t7p RCSB], [http://www.ebi.ac.uk/pdbsum/5t7p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t7p ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/LEC_PEA LEC_PEA]] D-mannose specific lectin.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Pisum arvense lectin (PAL), a legume protein belonging to the Vicieae tribe, is capable of specific recognition of mannose, glucose and its derivatives without altering its structure. In this work, the three-dimensional structure of PAL was determined by X-ray crystallography and studied in detail by a combination of molecular docking and molecular dynamics (MD). Crystals belonging to monoclinic space group P21 were grown by the vapor diffusion method at 293 K. The structure was solved at 2.16 A and was similar to that of other Vicieae lectins. The structure presented Rfactor and Rfree of 17.04% and 22.08%, respectively, with all acceptable geometric parameters. Molecular docking was performed to analyze interactions of the lectin with monosaccharides, disaccharides and high-mannose N-glycans. PAL demonstrated different affinities on carbohydrates, depending on bond orientation and glycosidic linkage present in ligands. Furthermore, the lectin interacted with representative N-glycans in a manner consistent with the biological effects described for Vicieae lectins. Carbohydrate-recognition domain (CRD) in-depth analysis was performed by MD, describing the behavior of CRD residues in complex with ligand, stability, flexibility of the protein over time, CRD volume and topology. This is a first report of its kind for a lectin of the Vicieae tribe.

-	~~Authors:~~ Pinto-Junior~~, V.R.~~, Santiago, ~~M.Q.~~, Osterne, ~~V.J.S.~~, ~~Silva-Filho~~, ~~J.C.~~, Rocha, ~~B.A.M.~~, ~~Delatorre~~, P., Nascimento, K.S.~~, Cavada, B~~.S.	+	Crystal structure of Pisum arvense seed lectin (PAL) and characterization of its interaction with carbohydrates by molecular docking and dynamics.,Pinto-Junior VR, Santiago MQ, Nobre CB, Osterne VJS, Leal RB, Cajazeiras JB, Lossio CF, Rocha BAM, Martins MGQ, Nobre CAS, Silva MTL, Nascimento KS, Cavada BS Arch Biochem Biophys. 2017 Jul 25;630:27-37. doi: 10.1016/j.abb.2017.07.013. PMID:28754321<ref>PMID:28754321</ref>

-	~~Description: Crystal structure~~ of ~~Pisum arvense lectin (PAL) complexed with X-Man~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Nascimento, K~~.S]]	+	<div class="pdbe-citations 5t7p" style="background-color:#fffaf0;"></div>
-	~~[[Category: Silva-Filho, J~~.~~C]]~~	+	== References ==
-	~~[[Category: Pinto~~-~~Junior, V.R]]~~	+	<references/>
-	~~[[Category~~: ~~Santiago, M.Q]]~~	+	__TOC__
-	[[Category: ~~Osterne, V.J.S~~]]	+	</StructureSection>
-	[[Category: Cavada, B.S]]	+	[[Category: Pisum sativum]]
-	~~[[Category: Rocha, B.A.M~~]]	+	[[Category: Cavada, B S]]
	[[Category: Delatorre, P]]		[[Category: Delatorre, P]]
		+	[[Category: Nascimento, K S]]
		+	[[Category: Osterne, V J.S]]
		+	[[Category: Pinto-Junior, V R]]
		+	[[Category: Rocha, B A.M]]
		+	[[Category: Santiago, M Q]]
		+	[[Category: Silva-Filho, J C]]
		+	[[Category: Lectin]]
		+	[[Category: Pal]]
		+	[[Category: Pisum arvense]]
		+	[[Category: Sugar binding protein]]
		+	[[Category: X-man]]

OCA at 13:23, 9 March 2017

OCA — Thu, 09 Mar 2017 13:23:43 GMT

←Older revision		Revision as of 13:23, 9 March 2017
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	Description: Crystal structure of Pisum arvense lectin (PAL) complexed with X-Man		Description: Crystal structure of Pisum arvense lectin (PAL) complexed with X-Man
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Rocha, B.A.M]]
	[[Category: Nascimento, K.S]]		[[Category: Nascimento, K.S]]
	[[Category: Silva-Filho, J.C]]		[[Category: Silva-Filho, J.C]]
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	[[Category: Osterne, V.J.S]]		[[Category: Osterne, V.J.S]]
	[[Category: Cavada, B.S]]		[[Category: Cavada, B.S]]
		+	[[Category: Rocha, B.A.M]]
	[[Category: Delatorre, P]]		[[Category: Delatorre, P]]

OCA: Protected "5t7p" [edit=sysop:move=sysop]

OCA — Wed, 14 Sep 2016 14:06:19 GMT

Protected "5t7p" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:06, 14 September 2016

OCA: New page: '''Unreleased structure''' The entry 5t7p is ON HOLD until Paper Publication Authors: Pinto-Junior, V.R., Santiago, M.Q., Osterne, V.J.S., Silva-Filho, J.C., Rocha, B.A.M., Delatorre, P...

OCA — Wed, 14 Sep 2016 14:06:17 GMT

New page: '''Unreleased structure''' The entry 5t7p is ON HOLD until Paper Publication Authors: Pinto-Junior, V.R., Santiago, M.Q., Osterne, V.J.S., Silva-Filho, J.C., Rocha, B.A.M., Delatorre, P...

New page

'''Unreleased structure'''

The entry 5t7p is ON HOLD until Paper Publication

Authors: Pinto-Junior, V.R., Santiago, M.Q., Osterne, V.J.S., Silva-Filho, J.C., Rocha, B.A.M., Delatorre, P., Nascimento, K.S., Cavada, B.S.

Description: Crystal structure of Pisum arvense lectin (PAL) complexed with X-Man
[[Category: Unreleased Structures]]
[[Category: Rocha, B.A.M]]
[[Category: Nascimento, K.S]]
[[Category: Silva-Filho, J.C]]
[[Category: Pinto-Junior, V.R]]
[[Category: Santiago, M.Q]]
[[Category: Osterne, V.J.S]]
[[Category: Cavada, B.S]]
[[Category: Delatorre, P]]