1kpm - Revision history

OCA at 09:02, 16 August 2023

2023-08-16T09:02:20Z

←Older revision		Revision as of 09:02, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='1kpm' size='340' side='right'caption='[[1kpm]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1kpm' size='340' side='right'caption='[[1kpm]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kpm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Daboia_pulchella~~ Daboia pulchella]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fe7 1fe7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KPM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kpm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Daboia_russelii_pulchella Daboia russelii pulchella]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fe7 1fe7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KPM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>~~, ~~<scene name='pdbligand=VIT:VITAMIN+E'>VIT</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]] 1.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1fe7\|1fe7]], [[1fb2\|1fb2]], [[1cl5\|1cl5]], [[1jq8\|1jq8]], [[1jq9\|1jq9]], [[1fv0\|1fv0]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=VIT:VITAMIN+E'>VIT</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4]~~ </~~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=1kpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpm OCA], [https://pdbe.org/1kpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kpm RCSB], [https://www.ebi.ac.uk/pdbsum/1kpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kpm 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=1kpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpm OCA], [https://pdbe.org/1kpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kpm RCSB], [https://www.ebi.ac.uk/pdbsum/1kpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kpm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PA2B8_DABRR PA2B8_DABRR]] Snake venom phospholipase A2 (PLA2) that shows weak neurotoxicity and medium anticoagulant effects by binding to factor Xa (F10) and inhibiting the prothrombinase activity (IC(50) is 130 nM) (PubMed:18062812). It also damages vital organs such as lung, liver and kidney, displays edema-inducing activities when injected into the foot pads of mice and induces necrosis of muscle cells when injected into the thigh muscle. Has a low enzymatic activity. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:18062812</ref> <ref>PMID:2115497</ref> <ref>PMID:8835338</ref>	+	[https://www.uniprot.org/uniprot/PA2B8_DABRR PA2B8_DABRR] Snake venom phospholipase A2 (PLA2) that shows weak neurotoxicity and medium anticoagulant effects by binding to factor Xa (F10) and inhibiting the prothrombinase activity (IC(50) is 130 nM) (PubMed:18062812). It also damages vital organs such as lung, liver and kidney, displays edema-inducing activities when injected into the foot pads of mice and induces necrosis of muscle cells when injected into the thigh muscle. Has a low enzymatic activity. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:18062812</ref> <ref>PMID:2115497</ref> <ref>PMID:8835338</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Daboia pulchella]]	+	[[Category: Daboia russelii pulchella]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Betzel, C]]	+	[[Category: Betzel C]]
-	[[Category: Chandra, V]]	+	[[Category: Chandra V]]
-	[[Category: Jasti, J]]	+	[[Category: Jasti J]]
-	[[Category: Kaur, P]]	+	[[Category: Kaur P]]
-	[[Category: Singh~~, T P~~]]	+	[[Category: Singh TP]]
-	[[Category: Srinivasan, A]]	+	[[Category: Srinivasan A]]
-	~~[[Category: Daboia russelli pulchella]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inflammation]]~~	+
-	~~[[Category: Neurotoxic]]~~	+
-	~~[[Category: Phospholipase a2~~]]	+

OCA at 08:49, 21 April 2021

2021-04-21T08:49:41Z

←Older revision		Revision as of 08:49, 21 April 2021
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	<StructureSection load='1kpm' size='340' side='right'caption='[[1kpm]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1kpm' size='340' side='right'caption='[[1kpm]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kpm]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Daboia_pulchella Daboia pulchella]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fe7 1fe7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KPM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kpm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Daboia_pulchella Daboia pulchella]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fe7 1fe7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KPM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=VIT:VITAMIN+E'>VIT</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=VIT:VITAMIN+E'>VIT</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fe7\|1fe7]], [[1fb2\|1fb2]], [[1cl5\|1cl5]], [[1jq8\|1jq8]], [[1jq9\|1jq9]], [[1fv0\|1fv0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fe7\|1fe7]], [[1fb2\|1fb2]], [[1cl5\|1cl5]], [[1jq8\|1jq8]], [[1jq9\|1jq9]], [[1fv0\|1fv0]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] </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=1kpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpm OCA], [~~http~~://pdbe.org/1kpm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kpm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kpm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kpm 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=1kpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpm OCA], [https://pdbe.org/1kpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kpm RCSB], [https://www.ebi.ac.uk/pdbsum/1kpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kpm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PA2B8_DABRR PA2B8_DABRR]] Snake venom phospholipase A2 (PLA2) that shows weak neurotoxicity and medium anticoagulant effects by binding to factor Xa (F10) and inhibiting the prothrombinase activity (IC(50) is 130 nM) (PubMed:18062812). It also damages vital organs such as lung, liver and kidney, displays edema-inducing activities when injected into the foot pads of mice and induces necrosis of muscle cells when injected into the thigh muscle. Has a low enzymatic activity. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:18062812</ref> <ref>PMID:2115497</ref> <ref>PMID:8835338</ref>	+	[[https://www.uniprot.org/uniprot/PA2B8_DABRR PA2B8_DABRR]] Snake venom phospholipase A2 (PLA2) that shows weak neurotoxicity and medium anticoagulant effects by binding to factor Xa (F10) and inhibiting the prothrombinase activity (IC(50) is 130 nM) (PubMed:18062812). It also damages vital organs such as lung, liver and kidney, displays edema-inducing activities when injected into the foot pads of mice and induces necrosis of muscle cells when injected into the thigh muscle. Has a low enzymatic activity. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:18062812</ref> <ref>PMID:2115497</ref> <ref>PMID:8835338</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
-	*[[Phospholipase A2\|Phospholipase A2]]	+	*[[Phospholipase A2 3D structures\|Phospholipase A2 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:13, 17 July 2019

2019-07-17T13:13:57Z

←Older revision		Revision as of 13:13, 17 July 2019
Line 1:		Line 1:

	==First Structural Evidence of a Specific Inhibition of Phospholipase A2 by Vitamin E and its Implications in Inflammation: Crystal Structure of the Complex Formed between Phospholipase A2 and Vitamin E at 1.8 A Resolution.==		==First Structural Evidence of a Specific Inhibition of Phospholipase A2 by Vitamin E and its Implications in Inflammation: Crystal Structure of the Complex Formed between Phospholipase A2 and Vitamin E at 1.8 A Resolution.==
-	<StructureSection load='1kpm' size='340' side='right' caption='[[1kpm]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1kpm' size='340' side='right'caption='[[1kpm]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kpm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Daboia_pulchella Daboia pulchella]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fe7 1fe7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KPM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kpm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Daboia_pulchella Daboia pulchella]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fe7 1fe7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KPM FirstGlance]. <br>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kp/1kpm_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kp/1kpm_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 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Daboia pulchella]]		[[Category: Daboia pulchella]]
		+	[[Category: Large Structures]]
	[[Category: Betzel, C]]		[[Category: Betzel, C]]
	[[Category: Chandra, V]]		[[Category: Chandra, V]]

OCA at 15:32, 12 October 2017

2017-10-12T15:32:49Z

←Older revision		Revision as of 15:32, 12 October 2017
Line 1:		Line 1:
		+
	==First Structural Evidence of a Specific Inhibition of Phospholipase A2 by Vitamin E and its Implications in Inflammation: Crystal Structure of the Complex Formed between Phospholipase A2 and Vitamin E at 1.8 A Resolution.==		==First Structural Evidence of a Specific Inhibition of Phospholipase A2 by Vitamin E and its Implications in Inflammation: Crystal Structure of the Complex Formed between Phospholipase A2 and Vitamin E at 1.8 A Resolution.==
	<StructureSection load='1kpm' size='340' side='right' caption='[[1kpm]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1kpm' size='340' side='right' caption='[[1kpm]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fe7\|1fe7]], [[1fb2\|1fb2]], [[1cl5\|1cl5]], [[1jq8\|1jq8]], [[1jq9\|1jq9]], [[1fv0\|1fv0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fe7\|1fe7]], [[1fb2\|1fb2]], [[1cl5\|1cl5]], [[1jq8\|1jq8]], [[1jq9\|1jq9]], [[1fv0\|1fv0]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] </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=1kpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpm OCA], [http://pdbe.org/1kpm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kpm RCSB], [http://www.ebi.ac.uk/pdbsum/1kpm 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=1kpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpm OCA], [http://pdbe.org/1kpm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kpm RCSB], [http://www.ebi.ac.uk/pdbsum/1kpm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kpm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 04:22, 9 February 2016

2016-02-09T04:22:21Z

←Older revision		Revision as of 04:22, 9 February 2016
Line 18:		Line 18:
	<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=1kpm ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 18:35, 10 September 2015

2015-09-10T18:35:30Z

←Older revision		Revision as of 18:35, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1kpm' size='340' side='right' caption='[[1kpm]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1kpm' size='340' side='right' caption='[[1kpm]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kpm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Daboia_russellii_pulchella~~ Daboia ~~russellii~~ pulchella]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fe7 1fe7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KPM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kpm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Daboia_pulchella Daboia pulchella]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fe7 1fe7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KPM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=VIT:VITAMIN+E'>VIT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=VIT:VITAMIN+E'>VIT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fe7\|1fe7]], [[1fb2\|1fb2]], [[1cl5\|1cl5]], [[1jq8\|1jq8]], [[1jq9\|1jq9]], [[1fv0\|1fv0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fe7\|1fe7]], [[1fb2\|1fb2]], [[1cl5\|1cl5]], [[1jq8\|1jq8]], [[1jq9\|1jq9]], [[1fv0\|1fv0]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] </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=1kpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kpm RCSB], [http://www.ebi.ac.uk/pdbsum/1kpm 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=1kpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpm OCA], [http://pdbe.org/1kpm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kpm RCSB], [http://www.ebi.ac.uk/pdbsum/1kpm PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~PA28_DABRP PA28_DABRP~~]] Snake venom phospholipase A2 (PLA2) that shows weak neurotoxicity and medium anticoagulant effects by binding to factor Xa (F10) and inhibiting the prothrombinase activity (IC(50) is 130 nM) (PubMed:18062812). It also damages vital organs such as lung, liver and kidney, displays edema-inducing activities when injected into the foot pads of mice and induces necrosis of muscle cells when injected into the thigh muscle. Has a low enzymatic activity. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:~~8835338~~</ref> <ref>PMID:2115497</ref> <ref>PMID:~~18062812~~</ref>	+	[[http://www.uniprot.org/uniprot/PA2B8_DABRR PA2B8_DABRR]] Snake venom phospholipase A2 (PLA2) that shows weak neurotoxicity and medium anticoagulant effects by binding to factor Xa (F10) and inhibiting the prothrombinase activity (IC(50) is 130 nM) (PubMed:18062812). It also damages vital organs such as lung, liver and kidney, displays edema-inducing activities when injected into the foot pads of mice and induces necrosis of muscle cells when injected into the thigh muscle. Has a low enzymatic activity. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:18062812</ref> <ref>PMID:2115497</ref> <ref>PMID:8835338</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 28:
	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 1kpm" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Daboia ~~russellii~~ pulchella]]	+	[[Category: Daboia pulchella]]
	[[Category: Betzel, C]]		[[Category: Betzel, C]]
	[[Category: Chandra, V]]		[[Category: Chandra, V]]

OCA at 04:23, 25 December 2014

2014-12-25T04:23:54Z

←Older revision		Revision as of 04:23, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kpm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Daboia_russellii_pulchella Daboia russellii pulchella]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fe7 1fe7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KPM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kpm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Daboia_russellii_pulchella Daboia russellii pulchella]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fe7 1fe7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KPM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=VIT:VITAMIN+E'>VIT</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=VIT:VITAMIN+E'>VIT</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fe7\|1fe7]], [[1fb2\|1fb2]], [[1cl5\|1cl5]], [[1jq8\|1jq8]], [[1jq9\|1jq9]], [[1fv0\|1fv0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fe7\|1fe7]], [[1fb2\|1fb2]], [[1cl5\|1cl5]], [[1jq8\|1jq8]], [[1jq9\|1jq9]], [[1fv0\|1fv0]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] </span></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=1kpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kpm RCSB], [http://www.ebi.ac.uk/pdbsum/1kpm 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=1kpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kpm RCSB], [http://www.ebi.ac.uk/pdbsum/1kpm PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PA28_DABRP PA28_DABRP]] Snake venom phospholipase A2 (PLA2) that shows weak neurotoxicity and medium anticoagulant effects by binding to factor Xa (F10) and inhibiting the prothrombinase activity (IC(50) is 130 nM) (PubMed:18062812). It also damages vital organs such as lung, liver and kidney, displays edema-inducing activities when injected into the foot pads of mice and induces necrosis of muscle cells when injected into the thigh muscle. Has a low enzymatic activity. PLA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.<ref>PMID:8835338</ref> <ref>PMID:2115497</ref> <ref>PMID:18062812</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Daboia russellii pulchella]]		[[Category: Daboia russellii pulchella]]
-	[[Category: Betzel, C.]]	+	[[Category: Betzel, C]]
-	[[Category: Chandra, V.]]	+	[[Category: Chandra, V]]
-	[[Category: Jasti, J.]]	+	[[Category: Jasti, J]]
-	[[Category: Kaur, P.]]	+	[[Category: Kaur, P]]
-	[[Category: Singh, T P.]]	+	[[Category: Singh, T P]]
-	[[Category: Srinivasan, A.]]	+	[[Category: Srinivasan, A]]
	[[Category: Daboia russelli pulchella]]		[[Category: Daboia russelli pulchella]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 15:00, 28 September 2014

2014-09-28T15:00:26Z

←Older revision		Revision as of 15:00, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1kpm.~~png~~\|~~left~~\|200px]]	+	==First Structural Evidence of a Specific Inhibition of Phospholipase A2 by Vitamin E and its Implications in Inflammation: Crystal Structure of the Complex Formed between Phospholipase A2 and Vitamin E at 1.8 A Resolution.==
		+	<StructureSection load='1kpm' size='340' side='right' caption='[[1kpm]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kpm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Daboia_russellii_pulchella Daboia russellii pulchella]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fe7 1fe7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KPM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=VIT:VITAMIN+E'>VIT</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fe7\|1fe7]], [[1fb2\|1fb2]], [[1cl5\|1cl5]], [[1jq8\|1jq8]], [[1jq9\|1jq9]], [[1fv0\|1fv0]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] </span></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=1kpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kpm RCSB], [http://www.ebi.ac.uk/pdbsum/1kpm 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/kp/1kpm_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 ==
		+	This is the first structural evidence of alpha-tocopherol (alpha-TP) as a possible candidate against inflammation, as it inhibits phospholipase A2 specifically and effectively. The crystal structure of the complex formed between Vipera russelli phospholipase A2 and alpha-tocopherol has been determined and refined to a resolution of 1.8 A. The structure contains two molecules, A and B, of phospholipase A2 in the asymmetric unit, together with one alpha-tocopherol molecule, which is bound specifically to one of them. The phospholipase A2 molecules interact extensively with each other in the crystalline state. The two molecules were found in a stable association in the solution state as well, thus indicating their inherent tendency to remain together as a structural unit, leading to significant functional implications. In the crystal structure, the most important difference between the conformations of two molecules as a result of their association pertains to the orientation of Trp31. It may be noted that Trp31 is located at the mouth of the hydrophobic channel that forms the binding domain of the enzyme. The values of torsion angles (phi, psi, chi(1) and chi(2)) for both the backbone as well as for the side-chain of Trp31 in molecules A and B are -94 degrees, -30 degrees, -66 degrees, 116 degrees and -128 degrees, 170 degrees, -63 degrees, -81 degrees, respectively. The conformation of Trp31 in molecule A is suitable for binding, while that in B hinders the passage of the ligand to the binding site. Consequently, alpha-tocopherol is able to bind to molecule A only, while the binding site of molecule B contains three water molecules. In the complex, the aromatic moiety of alpha-tocopherol is placed in the large space at the active site of the enzyme, while the long hydrophobic channel in the enzyme is filled by hydrocarbon chain of alpha-tocopherol. The critical interactions between the enzyme and alpha-tocopherol are generated between the hydroxyl group of the six-membered ring of alpha-tocopherol and His48 N(delta1) and Asp49 O(delta1) as characteristic hydrogen bonds. The remaining part of alpha-tocopherol interacts extensively with the residues of the hydrophobic channel of the enzyme, giving rise to a number of hydrophobic interactions, resulting in the formation of a stable complex.

-	~~{{STRUCTURE_1kpm\| PDB=1kpm \| SCENE= }}~~	+	First structural evidence of a specific inhibition of phospholipase A2 by alpha-tocopherol (vitamin E) and its implications in inflammation: crystal structure of the complex formed between phospholipase A2 and alpha-tocopherol at 1.8 A resolution.,Chandra V, Jasti J, Kaur P, Betzel Ch, Srinivasan A, Singh TP J Mol Biol. 2002 Jul 5;320(2):215-22. PMID:12079380<ref>PMID:12079380</ref>

-	~~===First Structural Evidence of~~ a ~~Specific Inhibition of Phospholipase A2 by Vitamin E and its Implications in Inflammation: Crystal Structure~~ of the ~~Complex Formed between Phospholipase A2 and Vitamin E at 1~~.~~8 A Resolution~~.~~===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12079380}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1kpm]] is a 2 chain structure with sequence from [http:~~//en.wikipedia.org/wiki/Daboia_russellii_pulchella Daboia russellii pulchella]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fe7 1fe7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPM OCA].	+

	==See Also==		==See Also==
	*[[Phospholipase A2\|Phospholipase A2]]		*[[Phospholipase A2\|Phospholipase A2]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012079380<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Daboia russellii pulchella]]		[[Category: Daboia russellii pulchella]]
	[[Category: Betzel, C.]]		[[Category: Betzel, C.]]

OCA at 12:37, 20 October 2012

2012-10-20T12:37:51Z

←Older revision		Revision as of 12:37, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1kpm]] is a 2 chain structure ~~of [[Phospholipase A2]]~~ with sequence from [http://en.wikipedia.org/wiki/Daboia_russellii_pulchella Daboia russellii pulchella]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fe7 1fe7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPM OCA].	+	[[1kpm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Daboia_russellii_pulchella Daboia russellii pulchella]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fe7 1fe7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPM OCA].

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

OCA at 09:21, 26 July 2012

2012-07-26T09:21:12Z

←Older revision		Revision as of 09:21, 26 July 2012
Line 1:		Line 1:
	[[Image:1kpm.png\|left\|200px]]		[[Image:1kpm.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1kpm", 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_1kpm\| PDB=1kpm \| SCENE= }}		{{STRUCTURE_1kpm\| PDB=1kpm \| SCENE= }}

	===First Structural Evidence of a Specific Inhibition of Phospholipase A2 by Vitamin E and its Implications in Inflammation: Crystal Structure of the Complex Formed between Phospholipase A2 and Vitamin E at 1.8 A Resolution.===		===First Structural Evidence of a Specific Inhibition of Phospholipase A2 by Vitamin E and its Implications in Inflammation: Crystal Structure of the Complex Formed between Phospholipase A2 and Vitamin E at 1.8 A Resolution.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12079380}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12079380 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_12079380}}		{{ABSTRACT_PUBMED_12079380}}

Line 22:		Line 11:

	==See Also==		==See Also==
-	*[[Phospholipase A2]]	+	*[[Phospholipase A2\|Phospholipase A2]]

	==Reference==		==Reference==