1ayj - Revision history

OCA at 15:29, 13 March 2024

2024-03-13T15:29:36Z

←Older revision		Revision as of 15:29, 13 March 2024
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	==DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF RAPHANUS SATIVUS ANTIFUNGAL PROTEIN 1 (RS-AFP1) BY 1H NMR, 20 STRUCTURES==		==DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF RAPHANUS SATIVUS ANTIFUNGAL PROTEIN 1 (RS-AFP1) BY 1H NMR, 20 STRUCTURES==
-	<StructureSection load='1ayj' size='340' side='right'caption='[[1ayj~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='1ayj' size='340' side='right'caption='[[1ayj]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ayj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AYJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ayj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AYJ FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</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=1ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayj OCA], [https://pdbe.org/1ayj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ayj RCSB], [https://www.ebi.ac.uk/pdbsum/1ayj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ayj 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=1ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayj OCA], [https://pdbe.org/1ayj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ayj RCSB], [https://www.ebi.ac.uk/pdbsum/1ayj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ayj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~DEF1_SINAL DEF1_SINAL]~~] Possesses antifungal activity sensitive to inorganic cations.	+	[https://www.uniprot.org/uniprot/DEF1_RAPSA DEF1_RAPSA] Possesses antifungal activity sensitive to inorganic cations.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1ayj 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=1ayj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Raphanus sativus Antifungal Protein 1 (Rs-AFP1) is a 51 amino acid residue plant defensin isolated from radish (Raphanus sativus L.) seeds. The three-dimensional structure in aqueous solution has been determined from two-dimensional 1H NMR data recorded at 500 MHz using the DIANA/REDAC calculation protocols. Experimental constraints consisted of 787 interproton distances extracted from NOE cross-peaks, 89 torsional constraints from 106 vicinal interproton coupling constants and 32 stereospecific assignments of prochiral protons. Further refinement by simulated annealing resulted in a set of 20 structures having pairwise root-mean-square differences of 1.35(+/- 0.35) A over the backbone heavy atoms and 2.11(+/- 0.46) A over all heavy atoms. The molecule adopts a compact globular fold comprising an alpha-helix from Asn18 till Leu28 and a triple-stranded beta-sheet (beta 1 = Lys2-Arg6, beta 2 = His33-Tyr38 and beta 3 = His43-Pro50). The central strand of this beta-sheet is connected by two disulfide bridges (Cys21-Cys45 and Cys25-Cys47) to the alpha-helix. The connection between beta-strand 2 and 3 is formed by a type VIa beta-turn. Even the loop (Pro7 to Asn17) between beta-strand 1 and the alpha-helix is relatively well defined. The structure of Raphanus sativus Antifungal Protein 1 features all the characteristics of the "cysteine stabilized alpha beta motif". A comparison of the complete structure and of the regions important for interaction with the fungal receptor according to a mutational study, is made with the structure of gamma-thionin, a plant defensin that has no antifungal activity. It is concluded that this interaction is both electrostatic and specific, and some possible scenarios for the mode of action are given.
-
-	Determination of the three-dimensional solution structure of Raphanus sativus antifungal protein 1 by 1H NMR.,Fant F, Vranken W, Broekaert W, Borremans F J Mol Biol. 1998 May 29;279(1):257-70. PMID:9636715<ref>PMID:9636715</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ayj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Plant defensin\|Plant defensin]]		*[[Plant defensin\|Plant defensin]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Raphanus sativus var. niger]]		[[Category: Raphanus sativus var. niger]]
-	[[Category: Borremans~~, F A.M~~]]	+	[[Category: Borremans FAM]]
-	[[Category: Fant, F]]	+	[[Category: Fant F]]
-	~~[[Category: Cysteine-stabilized alfa/beta motif]]~~	+
-	~~[[Category: Fungicide]]~~	+
-	~~[[Category: Plant defensin~~]]	+

OCA at 09:16, 29 September 2021

2021-09-29T09:16:33Z

←Older revision		Revision as of 09:16, 29 September 2021
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	<StructureSection load='1ayj' size='340' side='right'caption='[[1ayj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1ayj' size='340' side='right'caption='[[1ayj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ayj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1AYJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ayj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AYJ FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</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=1ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayj OCA], [~~http~~://pdbe.org/1ayj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ayj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ayj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ayj 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=1ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayj OCA], [https://pdbe.org/1ayj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ayj RCSB], [https://www.ebi.ac.uk/pdbsum/1ayj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ayj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DEF1_SINAL DEF1_SINAL]] Possesses antifungal activity sensitive to inorganic cations.	+	[[https://www.uniprot.org/uniprot/DEF1_SINAL DEF1_SINAL]] Possesses antifungal activity sensitive to inorganic cations.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:51, 10 October 2019

2019-10-10T06:51:33Z

←Older revision		Revision as of 06:51, 10 October 2019
Line 1:		Line 1:

	==DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF RAPHANUS SATIVUS ANTIFUNGAL PROTEIN 1 (RS-AFP1) BY 1H NMR, 20 STRUCTURES==		==DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF RAPHANUS SATIVUS ANTIFUNGAL PROTEIN 1 (RS-AFP1) BY 1H NMR, 20 STRUCTURES==
-	<StructureSection load='1ayj' size='340' side='right' caption='[[1ayj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='1ayj' size='340' side='right'caption='[[1ayj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ayj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AYJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ayj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AYJ 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/ay/1ayj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ay/1ayj_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 1ayj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ayj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Plant defensin\|Plant defensin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Raphanus sativus var. niger]]		[[Category: Raphanus sativus var. niger]]
	[[Category: Borremans, F A.M]]		[[Category: Borremans, F A.M]]

OCA at 11:15, 22 November 2017

2017-11-22T11:15:09Z

←Older revision		Revision as of 11:15, 22 November 2017
Line 1:		Line 1:
		+
	==DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF RAPHANUS SATIVUS ANTIFUNGAL PROTEIN 1 (RS-AFP1) BY 1H NMR, 20 STRUCTURES==		==DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF RAPHANUS SATIVUS ANTIFUNGAL PROTEIN 1 (RS-AFP1) BY 1H NMR, 20 STRUCTURES==
	<StructureSection load='1ayj' size='340' side='right' caption='[[1ayj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1ayj' size='340' side='right' caption='[[1ayj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1ayj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AYJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ayj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AYJ FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</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=1ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayj OCA], [http://pdbe.org/1ayj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ayj RCSB], [http://www.ebi.ac.uk/pdbsum/1ayj 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=1ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayj OCA], [http://pdbe.org/1ayj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ayj RCSB], [http://www.ebi.ac.uk/pdbsum/1ayj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ayj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1ayj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ayj" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Plant defensin\|Plant defensin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:35, 9 February 2016

2016-02-09T02:35:48Z

←Older revision		Revision as of 02:35, 9 February 2016
Line 16:		Line 16:
	<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=1ayj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:46, 10 September 2015

2015-09-10T17:46:37Z

←Older revision		Revision as of 17:46, 10 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1ayj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AYJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ayj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AYJ FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</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=1ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ayj RCSB], [http://www.ebi.ac.uk/pdbsum/1ayj 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=1ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayj OCA], [http://pdbe.org/1ayj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ayj RCSB], [http://www.ebi.ac.uk/pdbsum/1ayj PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~AFP1_SINAL AFP1_SINAL~~]] Possesses antifungal activity sensitive to inorganic cations.	+	[[http://www.uniprot.org/uniprot/DEF1_SINAL DEF1_SINAL]] Possesses antifungal activity sensitive to inorganic cations.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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 1ayj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 03:49, 25 December 2014

2014-12-25T03:49:27Z

←Older revision		Revision as of 03:49, 25 December 2014
Line 6:		Line 6:
	<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=1ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ayj RCSB], [http://www.ebi.ac.uk/pdbsum/1ayj 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=1ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ayj RCSB], [http://www.ebi.ac.uk/pdbsum/1ayj PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AFP1_SINAL AFP1_SINAL]] Possesses antifungal activity sensitive to inorganic cations.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:44, 22 December 2014

2014-12-22T10:44:32Z

←Older revision		Revision as of 10:44, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ayj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AYJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ayj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AYJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</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=1ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ayj RCSB], [http://www.ebi.ac.uk/pdbsum/1ayj 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=1ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ayj RCSB], [http://www.ebi.ac.uk/pdbsum/1ayj PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Raphanus sativus var. niger]]		[[Category: Raphanus sativus var. niger]]
-	[[Category: Borremans, F A.M.]]	+	[[Category: Borremans, F A.M]]
-	[[Category: Fant, F.]]	+	[[Category: Fant, F]]
	[[Category: Cysteine-stabilized alfa/beta motif]]		[[Category: Cysteine-stabilized alfa/beta motif]]
	[[Category: Fungicide]]		[[Category: Fungicide]]
	[[Category: Plant defensin]]		[[Category: Plant defensin]]

OCA at 03:18, 7 August 2014

2014-08-07T03:18:35Z

←Older revision		Revision as of 03:18, 7 August 2014
Line 1:		Line 1:
-	[[~~Image~~:1ayj.~~png\|left~~\|200px]]	+	==DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF RAPHANUS SATIVUS ANTIFUNGAL PROTEIN 1 (RS-AFP1) BY 1H NMR, 20 STRUCTURES==
		+	<StructureSection load='1ayj' size='340' side='right' caption='[[1ayj]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ayj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AYJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</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=1ayj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ayj RCSB], [http://www.ebi.ac.uk/pdbsum/1ayj 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/ay/1ayj_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 ==
		+	Raphanus sativus Antifungal Protein 1 (Rs-AFP1) is a 51 amino acid residue plant defensin isolated from radish (Raphanus sativus L.) seeds. The three-dimensional structure in aqueous solution has been determined from two-dimensional 1H NMR data recorded at 500 MHz using the DIANA/REDAC calculation protocols. Experimental constraints consisted of 787 interproton distances extracted from NOE cross-peaks, 89 torsional constraints from 106 vicinal interproton coupling constants and 32 stereospecific assignments of prochiral protons. Further refinement by simulated annealing resulted in a set of 20 structures having pairwise root-mean-square differences of 1.35(+/- 0.35) A over the backbone heavy atoms and 2.11(+/- 0.46) A over all heavy atoms. The molecule adopts a compact globular fold comprising an alpha-helix from Asn18 till Leu28 and a triple-stranded beta-sheet (beta 1 = Lys2-Arg6, beta 2 = His33-Tyr38 and beta 3 = His43-Pro50). The central strand of this beta-sheet is connected by two disulfide bridges (Cys21-Cys45 and Cys25-Cys47) to the alpha-helix. The connection between beta-strand 2 and 3 is formed by a type VIa beta-turn. Even the loop (Pro7 to Asn17) between beta-strand 1 and the alpha-helix is relatively well defined. The structure of Raphanus sativus Antifungal Protein 1 features all the characteristics of the "cysteine stabilized alpha beta motif". A comparison of the complete structure and of the regions important for interaction with the fungal receptor according to a mutational study, is made with the structure of gamma-thionin, a plant defensin that has no antifungal activity. It is concluded that this interaction is both electrostatic and specific, and some possible scenarios for the mode of action are given.

-	~~{{STRUCTURE_1ayj\| PDB=1ayj \| SCENE= }}~~	+	Determination of the three-dimensional solution structure of Raphanus sativus antifungal protein 1 by 1H NMR.,Fant F, Vranken W, Broekaert W, Borremans F J Mol Biol. 1998 May 29;279(1):257-70. PMID:9636715<ref>PMID:9636715</ref>

-	~~===DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF RAPHANUS SATIVUS ANTIFUNGAL PROTEIN 1 (RS-AFP1) BY 1H NMR~~, ~~20 STRUCTURES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9636715}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ayj]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Raphanus_sativus_var~~.~~_niger Raphanus sativus var. niger]. Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA].~~	+

	==See Also==		==See Also==
	*[[Plant defensin\|Plant defensin]]		*[[Plant defensin\|Plant defensin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:009636715<~~/~~ref~~><~~ref group="xtra">PMID:011734033</ref><ref group="xtra">PMID:012011089</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Raphanus sativus var. niger]]		[[Category: Raphanus sativus var. niger]]
	[[Category: Borremans, F A.M.]]		[[Category: Borremans, F A.M.]]

OCA at 12:20, 20 October 2012

2012-10-20T12:20:39Z

←Older revision		Revision as of 12:20, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1ayj]] is a 1 chain structure ~~of [[Plant defensin]]~~ with sequence from [http://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA].	+	[[1ayj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Raphanus_sativus_var._niger Raphanus sativus var. niger]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYJ OCA].

	==See Also==		==See Also==