3dpf: Difference between revisions

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 ==Crystal structure of the complex between MMP-8 and a non-zinc chelating inhibitor==
-<StructureSection load='3dpf' size='340' side='right' caption='[[3dpf]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='3dpf' size='340' side='right'caption='[[3dpf]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3dpf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3dpf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DPF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AXB:N-{[2-(2-AMINO-3,4-DIOXOCYCLOBUT-1-EN-1-YL)-1,2,3,4-TETRAHYDROISOQUINOLIN-7-YL]METHYL}-4-OXO-3,5,6,8-TETRAHYDRO-4H-THIOPYRANO[4,3 4,5]THIENO[2,3-D]PYRIMIDINE-2-CARBOXAMIDE+7,7-DIOXIDE'>AXB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HAE:ACETOHYDROXAMIC+ACID'>HAE</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3dpe|3dpe]], [[3dng|3dng]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AXB:N-{[2-(2-AMINO-3,4-DIOXOCYCLOBUT-1-EN-1-YL)-1,2,3,4-TETRAHYDROISOQUINOLIN-7-YL]METHYL}-4-OXO-3,5,6,8-TETRAHYDRO-4H-THIOPYRANO[4,3 4,5]THIENO[2,3-D]PYRIMIDINE-2-CARBOXAMIDE+7,7-DIOXIDE'>AXB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HAE:ACETOHYDROXAMIC+ACID'>HAE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MMP8, CLG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3dpf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpf OCA], [https://pdbe.org/3dpf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dpf RCSB], [https://www.ebi.ac.uk/pdbsum/3dpf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpf ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Neutrophil_collagenase Neutrophil collagenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.34 3.4.24.34] </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=3dpf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dpf OCA], [http://pdbe.org/3dpf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dpf RCSB], [http://www.ebi.ac.uk/pdbsum/3dpf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dpf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MMP8_HUMAN MMP8_HUMAN]] Can degrade fibrillar type I, II, and III collagens.
+[https://www.uniprot.org/uniprot/MMP8_HUMAN MMP8_HUMAN] Can degrade fibrillar type I, II, and III collagens.
 == 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/dp/3dpf_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dp/3dpf_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 31: @@
 ==See Also==
-*[[Matrix metalloproteinase|Matrix metalloproteinase]]
+*[[Matrix metalloproteinase 3D structures|Matrix metalloproteinase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Neutrophil collagenase]]
+[[Category: Large Structures]]
-[[Category: Mazza, F]]
+[[Category: Mazza F]]
-[[Category: Montanari, R]]
+[[Category: Montanari R]]
-[[Category: Pochetti, G]]
+[[Category: Pochetti G]]
-[[Category: Collagen degradation]]
-[[Category: Extracellular matrix]]
-[[Category: Glycoprotein]]
-[[Category: Hydrolase]]
-[[Category: Metal-binding]]
-[[Category: Metalloprotease]]
-[[Category: Non-zinc chelating inhibitor]]
-[[Category: Protease]]
-[[Category: Secreted]]
-[[Category: Selective inhibition]]
-[[Category: Zymogen]]