3i03 - Revision history

OCA at 07:34, 6 September 2023

OCA — Wed, 06 Sep 2023 07:34:49 GMT

←Older revision		Revision as of 07:34, 6 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3i03]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bothrops_jararacussu Bothrops jararacussu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I03 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I03 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3i03]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bothrops_jararacussu Bothrops jararacussu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I03 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I03 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>~~, ~~<scene name='pdbligand=PBP:~~1~~-(4-BROMO-PHENYL)-ETHANONE'>PBP</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]] 1.48Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3hzw\|3hzw]]~~, ~~[[3hzd\|3hzd]], [[2q2j\|2q2j]], [[3cxi\|3cxi]], [[3cyl\|3cyl]], [[1y4l\|1y4l]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=PBP:1-(4-BROMO-PHENYL)-ETHANONE'>PBP</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=3i03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i03 OCA], [https://pdbe.org/3i03 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i03 RCSB], [https://www.ebi.ac.uk/pdbsum/3i03 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i03 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=3i03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i03 OCA], [https://pdbe.org/3i03 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i03 RCSB], [https://www.ebi.ac.uk/pdbsum/3i03 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i03 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~PA2B1_BOTJR PA2B1_BOTJR]~~] Snake venom phospholipase A2 homolog that lacks enzymatic activity. In ~~vivo~~, induces ~~muscle necrosis~~, ~~accompanied by polymorphonuclear cell infiltration~~, and ~~edema~~ in the ~~mouse paw~~. ~~Damages~~ artificial and myoblast membranes by a calcium-independent mechanism~~. Has~~ bactericidal activity.<ref>PMID:~~3176051~~</ref> <ref>PMID:~~11018293~~</ref> <ref>PMID:~~11829743~~</ref> <ref>PMID:~~12079495~~</ref> <ref>PMID:17346668</ref> <ref>PMID:18160090</ref> <ref>PMID:~~17157889~~</ref>	+	[https://www.uniprot.org/uniprot/PA2H1_BOTJR PA2H1_BOTJR] Snake venom phospholipase A2 homolog that lacks enzymatic activity. Shows local myotoxic activity (PubMed:11018293, PubMed:12079495, PubMed:31906173). Induces inflammation, since it induces edema and leukocytes infiltration (PubMed:11018293, PubMed:31906173). In addition, it induces NLRP3 NLRP3, ASC (PYCARD), caspase-1 (CASP1), and IL-1beta (IL1B) gene expression in the gastrocnemius muscle, showing that it is able to activate NLRP3 inflammasome (PubMed:31906173). It also damages artificial and myoblast membranes by a calcium-independent mechanism, has bactericidal activity, and induces neuromuscular blockade (PubMed:27531710). A model of myotoxic mechanism has been proposed: an apo Lys49-PLA2 is activated by the entrance of a hydrophobic molecule (e.g. fatty acid) at the hydrophobic channel of the protein leading to a reorientation of a monomer (PubMed:27531710) (By similarity). This reorientation causes a transition between 'inactive' to 'active' states, causing alignment of C-terminal and membrane-docking sites (MDoS) side-by-side and putting the membrane-disruption sites (MDiS) in the same plane, exposed to solvent and in a symmetric position for both monomers (PubMed:27531710) (By similarity). The MDoS region stabilizes the toxin on membrane by the interaction of charged residues with phospholipid head groups (PubMed:27531710) (By similarity). Subsequently, the MDiS region destabilizes the membrane with penetration of hydrophobic residues (PubMed:27531710) (By similarity). This insertion causes a disorganization of the membrane, allowing an uncontrolled influx of ions (i.e. calcium and sodium), and eventually triggering irreversible intracellular alterations and cell death (PubMed:27531710) (By similarity).[UniProtKB:I6L8L6]<ref>PMID:11018293</ref> <ref>PMID:11829743</ref> <ref>PMID:12079495</ref> <ref>PMID:17157889</ref> <ref>PMID:17346668</ref> <ref>PMID:18160090</ref> <ref>PMID:27531710</ref> <ref>PMID:3176051</ref> <ref>PMID:31906173</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 39:		Line 39:
	[[Category: Bothrops jararacussu]]		[[Category: Bothrops jararacussu]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fernandes~~, C A.H~~]]	+	[[Category: Fernandes CAH]]
-	[[Category: Fontes~~, M R.M~~]]	+	[[Category: Fontes MRM]]
-	[[Category: Marchi-Salvador~~, D P~~]]	+	[[Category: Marchi-Salvador DP]]
-	[[Category: Soares~~, A M]]~~	+	[[Category: Soares AM]]
-	~~[[Category: Antibiotic]]~~	+
-	~~[[Category: Antimicrobial]]~~	+
-	~~[[Category: Bothropstoxin-i]]~~	+
-	~~[[Category: Disulfide bond]]~~	+
-	~~[[Category: Lys49-pla2]]~~	+
-	~~[[Category: Myotoxicity]]~~	+
-	~~[[Category: Myotoxin]]~~	+
-	~~[[Category: P-bromophenacyl bromide]]~~	+
-	~~[[Category: Phospholipase homologue]]~~	+
-	~~[[Category: Secreted]]~~	+
-	~~[[Category: Toxin~~]]	+

OCA at 11:19, 6 April 2022

OCA — Wed, 06 Apr 2022 11:19:17 GMT

←Older revision		Revision as of 11:19, 6 April 2022
Line 3:		Line 3:
	<StructureSection load='3i03' size='340' side='right'caption='[[3i03]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='3i03' size='340' side='right'caption='[[3i03]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i03]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bothrops_jararacussu Bothrops jararacussu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I03 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3I03 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i03]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bothrops_jararacussu Bothrops jararacussu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I03 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I03 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=PBP:1-(4-BROMO-PHENYL)-ETHANONE'>PBP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=PBP:1-(4-BROMO-PHENYL)-ETHANONE'>PBP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hzw\|3hzw]], [[3hzd\|3hzd]], [[2q2j\|2q2j]], [[3cxi\|3cxi]], [[3cyl\|3cyl]], [[1y4l\|1y4l]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3hzw\|3hzw]], [[3hzd\|3hzd]], [[2q2j\|2q2j]], [[3cxi\|3cxi]], [[3cyl\|3cyl]], [[1y4l\|1y4l]]</div></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=3i03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i03 OCA], [~~http~~://pdbe.org/3i03 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3i03 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3i03 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3i03 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=3i03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i03 OCA], [https://pdbe.org/3i03 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i03 RCSB], [https://www.ebi.ac.uk/pdbsum/3i03 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i03 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PA2B1_BOTJR PA2B1_BOTJR]] Snake venom phospholipase A2 homolog that lacks enzymatic activity. In vivo, induces muscle necrosis, accompanied by polymorphonuclear cell infiltration, and edema in the mouse paw. Damages artificial and myoblast membranes by a calcium-independent mechanism. Has bactericidal activity.<ref>PMID:3176051</ref> <ref>PMID:11018293</ref> <ref>PMID:11829743</ref> <ref>PMID:12079495</ref> <ref>PMID:17346668</ref> <ref>PMID:18160090</ref> <ref>PMID:17157889</ref>	+	[[https://www.uniprot.org/uniprot/PA2B1_BOTJR PA2B1_BOTJR]] Snake venom phospholipase A2 homolog that lacks enzymatic activity. In vivo, induces muscle necrosis, accompanied by polymorphonuclear cell infiltration, and edema in the mouse paw. Damages artificial and myoblast membranes by a calcium-independent mechanism. Has bactericidal activity.<ref>PMID:3176051</ref> <ref>PMID:11018293</ref> <ref>PMID:11829743</ref> <ref>PMID:12079495</ref> <ref>PMID:17346668</ref> <ref>PMID:18160090</ref> <ref>PMID:17157889</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	==See Also==		==See Also==
	*[[Phospholipase A2 3D structures\|Phospholipase A2 3D structures]]		*[[Phospholipase A2 3D structures\|Phospholipase A2 3D structures]]
		+	*[[Phospholipase A2 homolog\|Phospholipase A2 homolog]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:13, 27 November 2019

OCA — Wed, 27 Nov 2019 07:13:24 GMT

←Older revision		Revision as of 07:13, 27 November 2019
Line 1:		Line 1:

	==Crystal structure of bothropstoxin-I chemically modified by p-bromophenacyl bromide (BPB) - monomeric form at a high resolution==		==Crystal structure of bothropstoxin-I chemically modified by p-bromophenacyl bromide (BPB) - monomeric form at a high resolution==
-	<StructureSection load='3i03' size='340' side='right' caption='[[3i03]], [[Resolution\|resolution]] 1.48Å' scene=''>	+	<StructureSection load='3i03' size='340' side='right'caption='[[3i03]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3i03]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bothrops_jararacussu Bothrops jararacussu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I03 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I03 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3i03]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bothrops_jararacussu Bothrops jararacussu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I03 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I03 FirstGlance]. <br>
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Phospholipase A2\|Phospholipase A2]]	+	*[[Phospholipase A2 3D structures\|Phospholipase A2 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Bothrops jararacussu]]		[[Category: Bothrops jararacussu]]
		+	[[Category: Large Structures]]
	[[Category: Fernandes, C A.H]]		[[Category: Fernandes, C A.H]]
	[[Category: Fontes, M R.M]]		[[Category: Fontes, M R.M]]

OCA at 07:50, 12 December 2018

OCA — Wed, 12 Dec 2018 07:50:00 GMT

←Older revision		Revision as of 07:50, 12 December 2018
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i0/3i03_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i0/3i03_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>

OCA at 19:20, 4 August 2016

OCA — Thu, 04 Aug 2016 19:20:09 GMT

←Older revision		Revision as of 19:20, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of bothropstoxin-I chemically modified by p-bromophenacyl bromide (BPB) - monomeric form at a high resolution==		==Crystal structure of bothropstoxin-I chemically modified by p-bromophenacyl bromide (BPB) - monomeric form at a high resolution==
	<StructureSection load='3i03' size='340' side='right' caption='[[3i03]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='3i03' size='340' side='right' caption='[[3i03]], [[Resolution\|resolution]] 1.48Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=PBP:1-(4-BROMO-PHENYL)-ETHANONE'>PBP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=PBP:1-(4-BROMO-PHENYL)-ETHANONE'>PBP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hzw\|3hzw]], [[3hzd\|3hzd]], [[2q2j\|2q2j]], [[3cxi\|3cxi]], [[3cyl\|3cyl]], [[1y4l\|1y4l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hzw\|3hzw]], [[3hzd\|3hzd]], [[2q2j\|2q2j]], [[3cxi\|3cxi]], [[3cyl\|3cyl]], [[1y4l\|1y4l]]</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=3i03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i03 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i03 RCSB], [http://www.ebi.ac.uk/pdbsum/3i03 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=3i03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i03 OCA], [http://pdbe.org/3i03 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i03 RCSB], [http://www.ebi.ac.uk/pdbsum/3i03 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3i03 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		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=3i03 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		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 3i03" style="background-color:#fffaf0;"></div>

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

OCA at 18:40, 24 December 2014

OCA — Wed, 24 Dec 2014 18:40:14 GMT

←Older revision		Revision as of 18:40, 24 December 2014
Line 7:		Line 7:
	<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=3i03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i03 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i03 RCSB], [http://www.ebi.ac.uk/pdbsum/3i03 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=3i03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i03 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i03 RCSB], [http://www.ebi.ac.uk/pdbsum/3i03 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PA2B1_BOTJR PA2B1_BOTJR]] Snake venom phospholipase A2 homolog that lacks enzymatic activity. In vivo, induces muscle necrosis, accompanied by polymorphonuclear cell infiltration, and edema in the mouse paw. Damages artificial and myoblast membranes by a calcium-independent mechanism. Has bactericidal activity.<ref>PMID:3176051</ref> <ref>PMID:11018293</ref> <ref>PMID:11829743</ref> <ref>PMID:12079495</ref> <ref>PMID:17346668</ref> <ref>PMID:18160090</ref> <ref>PMID:17157889</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:00, 8 December 2014

OCA — Mon, 08 Dec 2014 09:00:13 GMT

←Older revision		Revision as of 09:00, 8 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3i03.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of bothropstoxin-I chemically modified by p-bromophenacyl bromide (BPB) - monomeric form at a high resolution==
		+	<StructureSection load='3i03' size='340' side='right' caption='[[3i03]], [[Resolution\|resolution]] 1.48Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3i03]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bothrops_jararacussu Bothrops jararacussu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I03 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I03 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=PBP:1-(4-BROMO-PHENYL)-ETHANONE'>PBP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hzw\|3hzw]], [[3hzd\|3hzd]], [[2q2j\|2q2j]], [[3cxi\|3cxi]], [[3cyl\|3cyl]], [[1y4l\|1y4l]]</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=3i03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i03 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i03 RCSB], [http://www.ebi.ac.uk/pdbsum/3i03 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/i0/3i03_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 ==
		+	Phospholipases A(2) (Asp49-PLA(2)s) are enzymes responsible for cellular membrane disruption through Ca(2+)-dependent hydrolysis of phospholipids. A class of these proteins (Lys49-PLA(2)s) does not show catalytic activity but can exert a pronounced local myotoxic effect that is not neutralized by serum therapy. In this work, we present five structures of Lys49-PLA(2)s from snakes of the Bothrops genus in apo form, complexed with PEG molecules and chemically modified by p-bromofenacil bromide (BPB), a classic inhibitor of PLA(2). We present herein an extensive structural analysis including: (i) the function of hydrophobic long-chain molecules as Lys49-PLA(2)s inhibitors, (ii) the role of Lys122, previously indicated as being responsible for Lys49-PLA(2)s catalytic inactivity and, (iii) a structural comparison of the Ca(2+)-binding loop region between Lys49 and Asp49-PLA(2)s. The Lys122 analysis of 30 different monomers for apo and complexed Lys49-PLA(2)s structures shows that this residue is very flexible and may bind to different carboxyl groups giving stability to the crystal structures. The structural comparisons of the Ca(2+)-binding loop region between Lys49 and Asp49-PLA(2)s reveal the importance of the Tyr28 residue conservation in Asp49-PLA(2)s to the integrity of this loop. The Tyr28 residue stabilizes this region by an interaction with Gly35 residue. In Lys49-PLA(2)s and low-catalytic Asp49-PLA(2)s this interaction does not occur, preventing the binding of Ca(2+).

-	~~{{STRUCTURE_3i03\| PDB=3i03 \| SCENE= }}~~	+	Comparison between apo and complexed structures of bothropstoxin-I reveals the role of Lys122 and Ca(2+)-binding loop region for the catalytically inactive Lys49-PLA(2)s.,Fernandes CA, Marchi-Salvador DP, Salvador GM, Silva MC, Costa TR, Soares AM, Fontes MR J Struct Biol. 2010 Apr 4. PMID:20371382<ref>PMID:20371382</ref>

-	~~===Crystal structure~~ of ~~bothropstoxin-I chemically modified by p-bromophenacyl bromide (BPB) - monomeric form at a high resolution===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20371382}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3i03]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bothrops_jararacussu Bothrops jararacussu]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3I03 OCA].~~	+

	==See Also==		==See Also==
	*[[Phospholipase A2\|Phospholipase A2]]		*[[Phospholipase A2\|Phospholipase A2]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020371382<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bothrops jararacussu]]		[[Category: Bothrops jararacussu]]
-	[[Category: Fernandes, C A.H.]]	+	[[Category: Fernandes, C A.H]]
-	[[Category: Fontes, M R.M.]]	+	[[Category: Fontes, M R.M]]
-	[[Category: Marchi-Salvador, D P.]]	+	[[Category: Marchi-Salvador, D P]]
-	[[Category: Soares, A M.]]	+	[[Category: Soares, A M]]
	[[Category: Antibiotic]]		[[Category: Antibiotic]]
	[[Category: Antimicrobial]]		[[Category: Antimicrobial]]

OCA at 08:03, 20 October 2012

OCA — Sat, 20 Oct 2012 08:03:29 GMT

←Older revision		Revision as of 08:03, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3i03]] is a 1 chain structure ~~of [[Phospholipase A2]]~~ with sequence from [http://en.wikipedia.org/wiki/Bothrops_jararacussu Bothrops jararacussu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I03 OCA].	+	[[3i03]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bothrops_jararacussu Bothrops jararacussu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I03 OCA].

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

OCA at 18:17, 25 July 2012

OCA — Wed, 25 Jul 2012 18:17:58 GMT

←Older revision		Revision as of 18:17, 25 July 2012
Line 1:		Line 1:
	[[Image:3i03.png\|left\|200px]]		[[Image:3i03.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3i03", 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.
-	-->
	{{STRUCTURE_3i03\| PDB=3i03 \| SCENE= }}		{{STRUCTURE_3i03\| PDB=3i03 \| SCENE= }}

	===Crystal structure of bothropstoxin-I chemically modified by p-bromophenacyl bromide (BPB) - monomeric form at a high resolution===		===Crystal structure of bothropstoxin-I chemically modified by p-bromophenacyl bromide (BPB) - monomeric form at a high resolution===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20371382}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20371382 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20371382}}		{{ABSTRACT_PUBMED_20371382}}

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

	==Reference==		==Reference==

OCA at 05:25, 30 November 2011

OCA — Wed, 30 Nov 2011 05:25:56 GMT

←Older revision		Revision as of 05:25, 30 November 2011
Line 25:		Line 25:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20371382~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020371382</ref><references group="xtra"/>
	[[Category: Bothrops jararacussu]]		[[Category: Bothrops jararacussu]]
	[[Category: Fernandes, C A.H.]]		[[Category: Fernandes, C A.H.]]