2w15 - Revision history

OCA at 15:40, 13 December 2023

OCA — Wed, 13 Dec 2023 15:40:11 GMT

←Older revision		Revision as of 15:40, 13 December 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2w15]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bothrops_asper Bothrops asper]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W15 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W15 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2w15]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bothrops_asper Bothrops asper]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W15 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W15 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=WR2:(2R,3R)-N^1^-[(1S)-2,2-DIMETHYL-1-(METHYLCARBAMOYL)PROPYL]-N^4^-HYDROXY-2-(2-METHYLPROPYL)-3-{[(1,3-THIAZOL-2-YLCARBONYL)AMINO]METHYL}BUTANEDIAMIDE'>WR2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.05Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=WR2:(2R,3R)-N^1^-[(1S)-2,2-DIMETHYL-1-(METHYLCARBAMOYL)PROPYL]-N^4^-HYDROXY-2-(2-METHYLPROPYL)-3-{[(1,3-THIAZOL-2-YLCARBONYL)AMINO]METHYL}BUTANEDIAMIDE'>WR2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1nd1\|1nd1]], [[2w13\|2w13]], [[2w14\|2w14]], [[2w12\|2w12]]</div></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=2w15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w15 OCA], [https://pdbe.org/2w15 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w15 RCSB], [https://www.ebi.ac.uk/pdbsum/2w15 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w15 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=2w15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w15 OCA], [https://pdbe.org/2w15 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w15 RCSB], [https://www.ebi.ac.uk/pdbsum/2w15 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w15 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/VM1B1_BOTAS VM1B1_BOTAS]] Zinc metalloprotease that exhibits a weak hemorrhagic activity (with a minimum hemorrhagic dose of 20 ug by intradermal and intramuscular injection into mice). The basal membrane components collagen (all chains of type IV) (COL4A4), laminin and nidogen are all degraded by this toxin (PubMed:23385358). Rapidly degrades the Aalpha-chain (FGA) of fibrinogen, and later on, degrades the Bbeta-chain (FGB) of fibrinogen (PubMed:7778126). Also activates the complement system, and induces rat neutrophil chemotaxis (PubMed:11200361). Induces edema in mouse food pad and a mild myotoxicity (PubMed:7778126).<ref>PMID:11200361</ref> <ref>PMID:20600221</ref> <ref>PMID:23385358</ref> <ref>PMID:7778126</ref>	+	[https://www.uniprot.org/uniprot/VM1B1_BOTAS VM1B1_BOTAS] Zinc metalloprotease that exhibits a weak hemorrhagic activity (with a minimum hemorrhagic dose of 20 ug by intradermal and intramuscular injection into mice). The basal membrane components collagen (all chains of type IV) (COL4A4), laminin and nidogen are all degraded by this toxin (PubMed:23385358). Rapidly degrades the Aalpha-chain (FGA) of fibrinogen, and later on, degrades the Bbeta-chain (FGB) of fibrinogen (PubMed:7778126). Also activates the complement system, and induces rat neutrophil chemotaxis (PubMed:11200361). Induces edema in mouse food pad and a mild myotoxicity (PubMed:7778126).<ref>PMID:11200361</ref> <ref>PMID:20600221</ref> <ref>PMID:23385358</ref> <ref>PMID:7778126</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 35:
	[[Category: Bothrops asper]]		[[Category: Bothrops asper]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gutierrez~~, J M~~]]	+	[[Category: Gutierrez JM]]
-	[[Category: Lingott~~, T J~~]]	+	[[Category: Lingott TJ]]
-	[[Category: Merfort, I]]	+	[[Category: Merfort I]]
-	[[Category: Schleberger, C]]	+	[[Category: Schleberger C]]
-	~~[[Category: Adamalysin]]~~	+
-	~~[[Category: Alpha-beta protein]]~~	+
-	~~[[Category: Chemotaxis]]~~	+
-	~~[[Category: Endopeptidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase inhibitor complex]]~~	+
-	~~[[Category: Hydrolase-inhibitor complex]]~~	+
-	~~[[Category: Matrixmetalloproteinase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Metalloprotease]]~~	+
-	~~[[Category: Metalloproteinase-inhibitor complex]]~~	+
-	~~[[Category: Metzincin]]~~	+
-	~~[[Category: P-i snake venom metalloproteinase]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Pyrrolidone carboxylic acid]]~~	+
-	~~[[Category: Secreted]]~~	+
-	~~[[Category: Toxin]]~~	+
-	~~[[Category: Tumor necrosis factor alpha converting enzyme]]~~	+
-	~~[[Category: Zinc]]~~	+
-	~~[[Category: Zinc-depending~~]]	+

OCA at 17:28, 15 December 2021

OCA — Wed, 15 Dec 2021 17:28:20 GMT

←Older revision		Revision as of 17:28, 15 December 2021
Line 3:		Line 3:
	<StructureSection load='2w15' size='340' side='right'caption='[[2w15]], [[Resolution\|resolution]] 1.05Å' scene=''>		<StructureSection load='2w15' size='340' side='right'caption='[[2w15]], [[Resolution\|resolution]] 1.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2w15]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bothrops_asper Bothrops asper]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W15 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2W15 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2w15]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bothrops_asper Bothrops asper]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W15 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W15 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=WR2:(2R,3R)-N^1^-[(1S)-2,2-DIMETHYL-1-(METHYLCARBAMOYL)PROPYL]-N^4^-HYDROXY-2-(2-METHYLPROPYL)-3-{[(1,3-THIAZOL-2-YLCARBONYL)AMINO]METHYL}BUTANEDIAMIDE'>WR2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=WR2:(2R,3R)-N^1^-[(1S)-2,2-DIMETHYL-1-(METHYLCARBAMOYL)PROPYL]-N^4^-HYDROXY-2-(2-METHYLPROPYL)-3-{[(1,3-THIAZOL-2-YLCARBONYL)AMINO]METHYL}BUTANEDIAMIDE'>WR2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nd1\|1nd1]], [[2w13\|2w13]], [[2w14\|2w14]], [[2w12\|2w12]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1nd1\|1nd1]], [[2w13\|2w13]], [[2w14\|2w14]], [[2w12\|2w12]]</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=2w15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w15 OCA], [~~http~~://pdbe.org/2w15 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2w15 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2w15 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2w15 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=2w15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w15 OCA], [https://pdbe.org/2w15 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w15 RCSB], [https://www.ebi.ac.uk/pdbsum/2w15 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w15 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/VM1B1_BOTAS VM1B1_BOTAS]] Zinc metalloprotease that exhibits a weak hemorrhagic activity (with a minimum hemorrhagic dose of 20 ug by intradermal and intramuscular injection into mice). The basal membrane components collagen (all chains of type IV) (COL4A4), laminin and nidogen are all degraded by this toxin (PubMed:23385358). Rapidly degrades the Aalpha-chain (FGA) of fibrinogen, and later on, degrades the Bbeta-chain (FGB) of fibrinogen (PubMed:7778126). Also activates the complement system, and induces rat neutrophil chemotaxis (PubMed:11200361). Induces edema in mouse food pad and a mild myotoxicity (PubMed:7778126).<ref>PMID:11200361</ref> <ref>PMID:20600221</ref> <ref>PMID:23385358</ref> <ref>PMID:7778126</ref>	+	[[https://www.uniprot.org/uniprot/VM1B1_BOTAS VM1B1_BOTAS]] Zinc metalloprotease that exhibits a weak hemorrhagic activity (with a minimum hemorrhagic dose of 20 ug by intradermal and intramuscular injection into mice). The basal membrane components collagen (all chains of type IV) (COL4A4), laminin and nidogen are all degraded by this toxin (PubMed:23385358). Rapidly degrades the Aalpha-chain (FGA) of fibrinogen, and later on, degrades the Bbeta-chain (FGB) of fibrinogen (PubMed:7778126). Also activates the complement system, and induces rat neutrophil chemotaxis (PubMed:11200361). Induces edema in mouse food pad and a mild myotoxicity (PubMed:7778126).<ref>PMID:11200361</ref> <ref>PMID:20600221</ref> <ref>PMID:23385358</ref> <ref>PMID:7778126</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:40, 11 March 2020

OCA — Wed, 11 Mar 2020 07:40:01 GMT

←Older revision		Revision as of 07:40, 11 March 2020
Line 1:		Line 1:

	==High-resolution crystal structure of the P-I snake venom metalloproteinase BaP1 in complex with a peptidomimetic: insights into inhibitor binding==		==High-resolution crystal structure of the P-I snake venom metalloproteinase BaP1 in complex with a peptidomimetic: insights into inhibitor binding==
-	<StructureSection load='2w15' size='340' side='right' caption='[[2w15]], [[Resolution\|resolution]] 1.05Å' scene=''>	+	<StructureSection load='2w15' size='340' side='right'caption='[[2w15]], [[Resolution\|resolution]] 1.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2w15]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bothrops_asper Bothrops asper]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W15 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2W15 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2w15]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bothrops_asper Bothrops asper]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W15 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2W15 FirstGlance]. <br>
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Bothrops asper]]		[[Category: Bothrops asper]]
		+	[[Category: Large Structures]]
	[[Category: Gutierrez, J M]]		[[Category: Gutierrez, J M]]
	[[Category: Lingott, T J]]		[[Category: Lingott, T J]]

OCA at 21:28, 19 September 2018

OCA — Wed, 19 Sep 2018 21:28:50 GMT

←Older revision		Revision as of 21:28, 19 September 2018
Line 1:		Line 1:
-	==~~HIGH~~-~~RESOLUTION CRYSTAL STRUCTURE OF THE~~ P-I ~~SNAKE VENOM METALLOPROTEINASE BAP1 IN COMPLEX WITH A PEPTIDOMIMETIC~~: ~~INSIGHTS INTO INHIBITOR BINDING~~==	+
		+	==High-resolution crystal structure of the P-I snake venom metalloproteinase BaP1 in complex with a peptidomimetic: insights into inhibitor binding==
	<StructureSection load='2w15' size='340' side='right' caption='[[2w15]], [[Resolution\|resolution]] 1.05Å' scene=''>		<StructureSection load='2w15' size='340' side='right' caption='[[2w15]], [[Resolution\|resolution]] 1.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 6:		Line 7:
	<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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nd1\|1nd1]], [[2w13\|2w13]], [[2w14\|2w14]], [[2w12\|2w12]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nd1\|1nd1]], [[2w13\|2w13]], [[2w14\|2w14]], [[2w12\|2w12]]</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=2w15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w15 OCA], [http://pdbe.org/2w15 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w15 RCSB], [http://www.ebi.ac.uk/pdbsum/2w15 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=2w15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w15 OCA], [http://pdbe.org/2w15 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w15 RCSB], [http://www.ebi.ac.uk/pdbsum/2w15 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2w15 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w1/2w15_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w1/2w15_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 56:		Line 57:
	[[Category: Toxin]]		[[Category: Toxin]]
	[[Category: Tumor necrosis factor alpha converting enzyme]]		[[Category: Tumor necrosis factor alpha converting enzyme]]
		+	[[Category: Zinc]]
	[[Category: Zinc-depending]]		[[Category: Zinc-depending]]

OCA at 15:52, 8 February 2016

OCA — Mon, 08 Feb 2016 15:52:21 GMT

←Older revision		Revision as of 15:52, 8 February 2016
Line 6:		Line 6:
	<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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nd1\|1nd1]], [[2w13\|2w13]], [[2w14\|2w14]], [[2w12\|2w12]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nd1\|1nd1]], [[2w13\|2w13]], [[2w14\|2w14]], [[2w12\|2w12]]</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=2w15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w15 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2w15 RCSB], [http://www.ebi.ac.uk/pdbsum/2w15 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=2w15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w15 OCA], [http://pdbe.org/2w15 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w15 RCSB], [http://www.ebi.ac.uk/pdbsum/2w15 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~VMBP1_BOTAS VMBP1_BOTAS~~]] Zinc metalloprotease that exhibits a weak hemorrhagic activity (with a minimum hemorrhagic dose of 20 ug by intradermal and intramuscular injection into mice). The basal membrane components collagen (all chains of type IV) (COL4A4), laminin and nidogen are all degraded by this toxin (PubMed:23385358). Rapidly degrades the Aalpha-chain (FGA) of fibrinogen, and later on, degrades the Bbeta-chain (FGB) of fibrinogen (PubMed:7778126). Also activates the complement system, and induces rat neutrophil chemotaxis (PubMed:11200361). Induces edema in mouse food pad and a mild myotoxicity (PubMed:7778126).<ref>PMID:~~7778126~~</ref> <ref>PMID:~~11200361~~</ref> <ref>PMID:~~20600221~~</ref> <ref>PMID:~~23385358~~</ref>	+	[[http://www.uniprot.org/uniprot/VM1B1_BOTAS VM1B1_BOTAS]] Zinc metalloprotease that exhibits a weak hemorrhagic activity (with a minimum hemorrhagic dose of 20 ug by intradermal and intramuscular injection into mice). The basal membrane components collagen (all chains of type IV) (COL4A4), laminin and nidogen are all degraded by this toxin (PubMed:23385358). Rapidly degrades the Aalpha-chain (FGA) of fibrinogen, and later on, degrades the Bbeta-chain (FGB) of fibrinogen (PubMed:7778126). Also activates the complement system, and induces rat neutrophil chemotaxis (PubMed:11200361). Induces edema in mouse food pad and a mild myotoxicity (PubMed:7778126).<ref>PMID:11200361</ref> <ref>PMID:20600221</ref> <ref>PMID:23385358</ref> <ref>PMID:7778126</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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=2w15 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 2w15" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 00:27, 25 December 2014

OCA — Thu, 25 Dec 2014 00:27:24 GMT

←Older revision		Revision as of 00:27, 25 December 2014
Line 8:		Line 8:
	<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=2w15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w15 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2w15 RCSB], [http://www.ebi.ac.uk/pdbsum/2w15 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=2w15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w15 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2w15 RCSB], [http://www.ebi.ac.uk/pdbsum/2w15 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VMBP1_BOTAS VMBP1_BOTAS]] Zinc metalloprotease that exhibits a weak hemorrhagic activity (with a minimum hemorrhagic dose of 20 ug by intradermal and intramuscular injection into mice). The basal membrane components collagen (all chains of type IV) (COL4A4), laminin and nidogen are all degraded by this toxin (PubMed:23385358). Rapidly degrades the Aalpha-chain (FGA) of fibrinogen, and later on, degrades the Bbeta-chain (FGB) of fibrinogen (PubMed:7778126). Also activates the complement system, and induces rat neutrophil chemotaxis (PubMed:11200361). Induces edema in mouse food pad and a mild myotoxicity (PubMed:7778126).<ref>PMID:7778126</ref> <ref>PMID:11200361</ref> <ref>PMID:20600221</ref> <ref>PMID:23385358</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Bothrops asper]]		[[Category: Bothrops asper]]
-	[[Category: Gutierrez, J M.]]	+	[[Category: Gutierrez, J M]]
-	[[Category: Lingott, T J.]]	+	[[Category: Lingott, T J]]
-	[[Category: Merfort, I.]]	+	[[Category: Merfort, I]]
-	[[Category: Schleberger, C.]]	+	[[Category: Schleberger, C]]
	[[Category: Adamalysin]]		[[Category: Adamalysin]]
	[[Category: Alpha-beta protein]]		[[Category: Alpha-beta protein]]

OCA at 06:57, 10 October 2014

OCA — Fri, 10 Oct 2014 06:57:32 GMT

←Older revision		Revision as of 06:57, 10 October 2014
Line 2:		Line 2:
	<StructureSection load='2w15' size='340' side='right' caption='[[2w15]], [[Resolution\|resolution]] 1.05Å' scene=''>		<StructureSection load='2w15' size='340' side='right' caption='[[2w15]], [[Resolution\|resolution]] 1.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2w15]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bothrops_asper Bothrops asper]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W15 OCA]. <br>	+	<table><tr><td colspan='2'>[[2w15]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bothrops_asper Bothrops asper]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W15 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2W15 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=WR2:(2R,3R)-N^1^-[(1S)-2,2-DIMETHYL-1-(METHYLCARBAMOYL)PROPYL]-N^4^-HYDROXY-2-(2-METHYLPROPYL)-3-{[(1,3-THIAZOL-2-YLCARBONYL)AMINO]METHYL}BUTANEDIAMIDE'>WR2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=WR2:(2R,3R)-N^1^-[(1S)-2,2-DIMETHYL-1-(METHYLCARBAMOYL)PROPYL]-N^4^-HYDROXY-2-(2-METHYLPROPYL)-3-{[(1,3-THIAZOL-2-YLCARBONYL)AMINO]METHYL}BUTANEDIAMIDE'>WR2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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 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>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nd1\|1nd1]], [[2w13\|2w13]], [[2w14\|2w14]], [[2w12\|2w12]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nd1\|1nd1]], [[2w13\|2w13]], [[2w14\|2w14]], [[2w12\|2w12]]</td></tr>
-	<tr~~><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class~~='~~plainlinks~~'~~>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2w15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w15 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2w15 RCSB], [http://www.ebi.ac.uk/pdbsum/2w15 PDBsum]</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=2w15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w15 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2w15 RCSB], [http://www.ebi.ac.uk/pdbsum/2w15 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 25:		Line 24:
	High-Resolution Crystal Structure of the Snake Venom Metalloproteinase BaP1 Complexed with a Peptidomimetic: Insight into Inhibitor Binding.,Lingott T, Schleberger C, Gutierrez JM, Merfort I Biochemistry. 2009 Jun 15. PMID:19485419<ref>PMID:19485419</ref>		High-Resolution Crystal Structure of the Snake Venom Metalloproteinase BaP1 Complexed with a Peptidomimetic: Insight into Inhibitor Binding.,Lingott T, Schleberger C, Gutierrez JM, Merfort I Biochemistry. 2009 Jun 15. PMID:19485419<ref>PMID:19485419</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==

OCA at 08:44, 7 May 2014

OCA — Wed, 07 May 2014 08:44:24 GMT

←Older revision		Revision as of 08:44, 7 May 2014
Line 1:		Line 1:
-	[[~~Image:~~2w15.~~png~~\|~~left~~\|200px]]	+	==HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE P-I SNAKE VENOM METALLOPROTEINASE BAP1 IN COMPLEX WITH A PEPTIDOMIMETIC: INSIGHTS INTO INHIBITOR BINDING==
		+	<StructureSection load='2w15' size='340' side='right' caption='[[2w15]], [[Resolution\|resolution]] 1.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2w15]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bothrops_asper Bothrops asper]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W15 OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=WR2:(2R,3R)-N^1^-[(1S)-2,2-DIMETHYL-1-(METHYLCARBAMOYL)PROPYL]-N^4^-HYDROXY-2-(2-METHYLPROPYL)-3-{[(1,3-THIAZOL-2-YLCARBONYL)AMINO]METHYL}BUTANEDIAMIDE'>WR2</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<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>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nd1\|1nd1]], [[2w13\|2w13]], [[2w14\|2w14]], [[2w12\|2w12]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2w15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w15 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2w15 RCSB], [http://www.ebi.ac.uk/pdbsum/2w15 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/w1/2w15_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 ==
		+	BaP1, a zinc-dependent endopeptidase belonging to the P-I class of snake venom metalloproteinases, exerts multiple tissue-damaging activities, leading to hemorrhage, myonecrosis, dermonecrosis, blistering, and edema. Interestingly, this metalloproteinase shows a high degree of structural homology with the catalytic domain of human adamalysins and matrix metalloproteinases, especially at the strictly conserved zinc binding motif and the so-called Met turn. This highlights BaP1 as an interesting model concerning inhibitor design for several medicinally important metalloproteinases, such as tumor necrosis factor alpha converting enzyme. Here, we report the first crystal structure of BaP1 complexed with a peptidomimetic inhibitor. Suitable crystals were obtained at four different pH values (4.6, 6.5, 7.5, and 8.0), and four high-resolution structures (1.46, 1.14, 1.08, and 1.05 A) were established. These structures and the detailed analysis of the structure-activity relationship of the bound inhibitor form a basis for the design of potent BaP1 inhibitors. The latter can be used for the treatment of local pathological effects caused by snake bites, mainly due to metalloproteinases such as BaP1. Besides, the high-resolution structure is an excellent starting point for the rational development of inhibitors for human metalloproteinases. The finding of a flexible loop region may have a great impact on further studies as to date little is known about the structural dependencies of the hemorrhagic activity of snake venom metalloproteinases.

-	<!--	+	High-Resolution Crystal Structure of the Snake Venom Metalloproteinase BaP1 Complexed with a Peptidomimetic: Insight into Inhibitor Binding.,Lingott T, Schleberger C, Gutierrez JM, Merfort I Biochemistry. 2009 Jun 15. PMID:19485419<ref>PMID:19485419</ref>
-	~~The line below this paragraph, containing "STRUCTURE_2w15", 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_2w15\| PDB=2w15 \| SCENE= }}~~	+

-	~~===HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE P-I SNAKE VENOM METALLOPROTEINASE BAP1 IN COMPLEX WITH A PEPTIDOMIMETIC: INSIGHTS INTO INHIBITOR BINDING===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_19485419}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 19485419 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_19485419}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2w15]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Bothrops_asper Bothrops asper]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W15 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019485419<~~/~~ref~~><~~ref group="xtra">PMID:014500885</ref><references group="xtra"~~/>	+
	[[Category: Bothrops asper]]		[[Category: Bothrops asper]]
	[[Category: Gutierrez, J M.]]		[[Category: Gutierrez, J M.]]

OCA at 05:17, 21 September 2011

OCA — Wed, 21 Sep 2011 05:17:40 GMT

←Older revision		Revision as of 05:17, 21 September 2011
Line 22:		Line 22:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19485419~~</ref><ref group="xtra">PMID:~~14500885~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019485419</ref><ref group="xtra">PMID:014500885</ref><references group="xtra"/>
	[[Category: Bothrops asper]]		[[Category: Bothrops asper]]
	[[Category: Gutierrez, J M.]]		[[Category: Gutierrez, J M.]]
Line 34:		Line 34:
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Hydrolase inhibitor complex]]		[[Category: Hydrolase inhibitor complex]]
-	[[Category: Hydrolase/inhibitor complex]]	+	[[Category: Hydrolase-inhibitor complex]]
	[[Category: Matrixmetalloproteinase]]		[[Category: Matrixmetalloproteinase]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Metalloprotease]]		[[Category: Metalloprotease]]
-	[[Category: Metalloproteinase/inhibitor complex]]	+	[[Category: Metalloproteinase-inhibitor complex]]
	[[Category: Metzincin]]		[[Category: Metzincin]]
	[[Category: P-i snake venom metalloproteinase]]		[[Category: P-i snake venom metalloproteinase]]
Line 46:		Line 46:
	[[Category: Toxin]]		[[Category: Toxin]]
	[[Category: Tumor necrosis factor alpha converting enzyme]]		[[Category: Tumor necrosis factor alpha converting enzyme]]
-	[[Category: Zinc]]
	[[Category: Zinc-depending]]		[[Category: Zinc-depending]]

OCA: Protected "2w15" [edit=sysop:move=sysop]

OCA — Tue, 15 Mar 2011 00:47:41 GMT

Protected "2w15" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:47, 15 March 2011