1gvu: Difference between revisions

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-{{Seed}}
-[[Image:1gvu.png|left|200px]]
-<!--
+==Endothiapepsin complex with H189==
-The line below this paragraph, containing "STRUCTURE_1gvu", creates the "Structure Box" on the page.
+<StructureSection load='1gvu' size='340' side='right'caption='[[1gvu]], [[Resolution|resolution]] 0.94&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'>[[1gvu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [https://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GVU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GVU 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]] 0.94&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=STA:STATINE'>STA</scene>, <scene name='pdbligand=SUI:(3-AMINO-2,5-DIOXO-1-PYRROLIDINYL)ACETIC+ACID'>SUI</scene></td></tr>
-{{STRUCTURE_1gvu|  PDB=1gvu  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gvu OCA], [https://pdbe.org/1gvu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gvu RCSB], [https://www.ebi.ac.uk/pdbsum/1gvu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gvu ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CARP_CRYPA CARP_CRYPA]
+== 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/gv/1gvu_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/main_output.php?pdb_ID=1gvu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Endothiapepsin is derived from the fungus Endothia parasitica and is a member of the aspartic proteinase class of enzymes. This class of enzyme is comprised of two structurally similar lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The three-dimensional structures of endothiapepsin bound to five transition state analogue inhibitors (H189, H256, CP-80,794, PD-129,541 and PD-130,328) have been solved at atomic resolution allowing full anisotropic modelling of each complex. The active sites of the five structures have been studied with a view to studying the catalytic mechanism of the aspartic proteinases by locating the active site protons by carboxyl bond length differences and electron density analysis. In the CP-80,794 structure there is excellent electron density for the hydrogen on the inhibitory statine hydroxyl group which forms a hydrogen bond with the inner oxygen of Asp32. The location of this proton has implications for the catalytic mechanism of the aspartic proteinases as it is consistent with the proposed mechanism in which Asp32 is the negatively charged aspartate. A number of short hydrogen bonds (approximately 2.6 A) with ESD values of around 0.01 A that may have a role in catalysis have been identified within the active site of each structure; the lengths of these bonds have been confirmed using NMR techniques. The possibility and implications of low barrier hydrogen bonds in the active site are considered.
-===ENDOTHIAPEPSIN COMPLEX WITH H189===
+Five atomic resolution structures of endothiapepsin inhibitor complexes: implications for the aspartic proteinase mechanism.,Coates L, Erskine PT, Crump MP, Wood SP, Cooper JB J Mol Biol. 2002 May 17;318(5):1405-15. PMID:12083527<ref>PMID:12083527</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1gvu" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12083527}}, adds the Publication Abstract to the page
+*[[Pepsin|Pepsin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12083527 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12083527}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Bos taurus]]
-GVU is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GVU OCA].
-==Reference==
-Five atomic resolution structures of endothiapepsin inhibitor complexes: implications for the aspartic proteinase mechanism., Coates L, Erskine PT, Crump MP, Wood SP, Cooper JB, J Mol Biol. 2002 May 17;318(5):1405-15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12083527 12083527]
 [[Category: Cryphonectria parasitica]]
-[[Category: Endothiapepsin]]
+[[Category: Large Structures]]
-[[Category: Protein complex]]
+[[Category: Coates L]]
-[[Category: Coates, L.]]
+[[Category: Cooper JB]]
-[[Category: Cooper, J B.]]
+[[Category: Crump MP]]
-[[Category: Crump, M P.]]
+[[Category: Erskine PT]]
-[[Category: Erskine, P T.]]
+[[Category: Wood SP]]
-[[Category: Wood, S P.]]
-[[Category: Anisotropic refinement,aspartyl p]]
-[[Category: Aspartic proteinase mechanism]]
-[[Category: Atomic resolution,hydrolase,z tetrahedral intermediate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 06:11:15 2008''