1nd1: Difference between revisions

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 ==Amino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities.==
-<StructureSection load='1nd1' size='340' side='right' caption='[[1nd1]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
+<StructureSection load='1nd1' size='340' side='right'caption='[[1nd1]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1nd1]] 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=1ND1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ND1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1nd1]] 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=1ND1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ND1 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 1.93&#8491;</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=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd1 OCA], [http://pdbe.org/1nd1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nd1 RCSB], [http://www.ebi.ac.uk/pdbsum/1nd1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nd1 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=1nd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nd1 OCA], [https://pdbe.org/1nd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nd1 RCSB], [https://www.ebi.ac.uk/pdbsum/1nd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nd1 ProSAT]</span></td></tr>
 </table>
 == 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 ==
 [[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/nd/1nd1_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nd/1nd1_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 34: / Line 34: @@
 </StructureSection>
 [[Category: Bothrops asper]]
-[[Category: Alape-Giron, A]]
+[[Category: Large Structures]]
-[[Category: Arni, R K]]
+[[Category: Alape-Giron A]]
-[[Category: Fox, J W]]
+[[Category: Arni RK]]
-[[Category: Gutierrez, J M]]
+[[Category: Fox JW]]
-[[Category: Kamiguti, A S]]
+[[Category: Gutierrez JM]]
-[[Category: Rucavado, A]]
+[[Category: Kamiguti AS]]
-[[Category: Shannon, J D]]
+[[Category: Rucavado A]]
-[[Category: Theakston, R D]]
+[[Category: Shannon JD]]
-[[Category: Valente, R H]]
+[[Category: Theakston RD]]
-[[Category: Watanabe, L]]
+[[Category: Valente RH]]
-[[Category: Metalloproteinase]]
+[[Category: Watanabe L]]
-[[Category: Snake venom]]
-[[Category: Three-disulfide]]
-[[Category: Toxin]]