4ape: Difference between revisions

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-[[Image:4ape.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_4ape", 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_4ape|  PDB=4ape  |  SCENE=  }}
-'''THE ACTIVE SITE OF ASPARTIC PROTEINASES'''
+==THE ACTIVE SITE OF ASPARTIC PROTEINASES==
+<StructureSection load='4ape' size='340' side='right'caption='[[4ape]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4ape]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Crypa Crypa]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2ape 2ape] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ape 1ape]. The December 2000 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Pepsin''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2000_12 10.2210/rcsb_pdb/mom_2000_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4APE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4APE FirstGlance]. <br>
+</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </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=4ape FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ape OCA], [http://pdbe.org/4ape PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ape RCSB], [http://www.ebi.ac.uk/pdbsum/4ape PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ape ProSAT]</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/ap/4ape_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=4ape ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The active site of the aspartic proteinase, endothiapepsin, has been defined by X-ray analysis and restrained least-squares refinement at 2.1 A resolution with a crystallographic agreement value of 0.16. The environments of the two catalytically important aspartyl groups are remarkably similar and the contributions of the NH2- and COOH-terminal domains to the catalytic centre are related by a local 2-fold axis. The carboxylates of the aspartyls share a hydrogen bond and have equivalent contacts to a bound water molecule or hydroxonium ion lying on the local diad. The main chains around 32 and 215 are connected by a novel interaction involving diad-related threonines. It is suggested that the two pKa values of the active site aspartyls arise from a structure not unlike that in maleic acid with a hydrogen-bonded intermediate species and a dicarboxylate characterised by electrostatic repulsions between the two negatively charged groups.
-==Overview==
+The active site of aspartic proteinases.,Pearl L, Blundell T FEBS Lett. 1984 Aug 20;174(1):96-101. PMID:6381096<ref>PMID:6381096</ref>
-The active site of the aspartic proteinase, endothiapepsin, has been defined by X-ray analysis and restrained least-squares refinement at 2.1 A resolution with a crystallographic agreement value of 0.16. The environments of the two catalytically important aspartyl groups are remarkably similar and the contributions of the NH2- and COOH-terminal domains to the catalytic centre are related by a local 2-fold axis. The carboxylates of the aspartyls share a hydrogen bond and have equivalent contacts to a bound water molecule or hydroxonium ion lying on the local diad. The main chains around 32 and 215 are connected by a novel interaction involving diad-related threonines. It is suggested that the two pKa values of the active site aspartyls arise from a structure not unlike that in maleic acid with a hydrogen-bonded intermediate species and a dicarboxylate characterised by electrostatic repulsions between the two negatively charged groups.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-APE is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. This structure supersedes the now removed PDB entries  and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ape 1ape]. The following page contains interesting information on the relation of 4APE with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb12_1.html Pepsin]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4APE OCA].
+</div>
+<div class="pdbe-citations 4ape" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-The active site of aspartic proteinases., Pearl L, Blundell T, FEBS Lett. 1984 Aug 20;174(1):96-101. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/6381096 6381096]
+*[[Pepsin|Pepsin]]
-[[Category: Cryphonectria parasitica]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Crypa]]
 [[Category: Endothiapepsin]]
+[[Category: Large Structures]]
 [[Category: Pepsin]]
-[[Category: Single protein]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Blundell, T L.]]
+[[Category: Blundell, T L]]
-[[Category: Cooper, J B.]]
+[[Category: Cooper, J B]]
-[[Category: Jenkins, J A.]]
+[[Category: Jenkins, J A]]
-[[Category: Pearl, L H.]]
+[[Category: Pearl, L H]]
-[[Category: Sewell, B T.]]
+[[Category: Sewell, B T]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 22:20:57 2008''