1fi8: Difference between revisions

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-{{Seed}}
-[[Image:1fi8.png|left|200px]]
-<!--
+==RAT GRANZYME B [N66Q] COMPLEXED TO ECOTIN [81-84 IEPD]==
-The line below this paragraph, containing "STRUCTURE_1fi8", creates the "Structure Box" on the page.
+<StructureSection load='1fi8' size='340' side='right'caption='[[1fi8]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1fi8]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FI8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FI8 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</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=1fi8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fi8 OCA], [https://pdbe.org/1fi8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fi8 RCSB], [https://www.ebi.ac.uk/pdbsum/1fi8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fi8 ProSAT]</span></td></tr>
-{{STRUCTURE_1fi8|  PDB=1fi8  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GRAB_RAT GRAB_RAT] This enzyme is necessary for target cell lysis in cell-mediated immune responses. It cleaves after Asp. Seems to be linked to an activation cascade of caspases (aspartate-specific cysteine proteases) responsible for apoptosis execution. Cleaves caspase-3, -7, -9 and 10 to give rise to active enzymes mediating apoptosis (By similarity).
+== 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/fi/1fi8_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=1fi8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Granzyme B is a serine protease of the chymotrypsin fold that mediates cell death by cytotoxic lymphocytes. It is a processing enzyme, requiring extended peptide substrates containing an Asp residue. The determinants that allow for this substrate specificity are revealed in the three-dimensional structure of granzyme B in complex with a macromolecular inhibitor. The primary specificity for Asp occurs through a side-on interaction with Arg 226, a buried Arg side chain of granzyme B. An additional nine amino acids make contact with the substrate and define the granzyme B extended substrate specificity profile. The substrate determinants found in this structure are shared by other members of this protein class and help to reveal the properties that define substrate specificity.
-===RAT GRANZYME B [N66Q] COMPLEXED TO ECOTIN [81-84 IEPD]===
+The structure of the pro-apoptotic protease granzyme B reveals the molecular determinants of its specificity.,Waugh SM, Harris JL, Fletterick R, Craik CS Nat Struct Biol. 2000 Sep;7(9):762-5. PMID:10966646<ref>PMID:10966646</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1fi8" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10966646}}, adds the Publication Abstract to the page
+*[[Ecotin|Ecotin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10966646 is the PubMed ID number.
+*[[Granzyme|Granzyme]]
--->
+== References ==
-{{ABSTRACT_PUBMED_10966646}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-FI8 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FI8 OCA].
-==Reference==
-The structure of the pro-apoptotic protease granzyme B reveals the molecular determinants of its specificity., Waugh SM, Harris JL, Fletterick R, Craik CS, Nat Struct Biol. 2000 Sep;7(9):762-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10966646 10966646]
 [[Category: Escherichia coli]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
 [[Category: Rattus norvegicus]]
-[[Category: Craik, C S.]]
+[[Category: Craik CS]]
-[[Category: Fletterick, R J.]]
+[[Category: Fletterick RJ]]
-[[Category: Harris, J L.]]
+[[Category: Harris JL]]
-[[Category: Waugh, S M.]]
+[[Category: Waugh SM]]
-[[Category: Beta strand structure]]
-[[Category: Chymotrypsin fold]]
-[[Category: Ecotin]]
-[[Category: Granzyme b]]
-[[Category: Protease substrate interaction]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 03:17:16 2008''