2jjj: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2jjj.png|left|200px]]
-<!--
+==Endothiapepsin in complex with a gem-diol inhibitor.==
-The line below this paragraph, containing "STRUCTURE_2jjj", creates the "Structure Box" on the page.
+<StructureSection load='2jjj' size='340' side='right'caption='[[2jjj]], [[Resolution|resolution]] 1.00&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'>[[2jjj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JJJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JJJ 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]] 1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0QS:N~2~-[(2R)-2-BENZYL-3-(TERT-BUTYLSULFONYL)PROPANOYL]-N-{(1R)-1-(CYCLOHEXYLMETHYL)-3,3-DIFLUORO-2,2-DIHYDROXY-4-[(2-MORPHOLIN-4-YLETHYL)AMINO]-4-OXOBUTYL}-3-(1H-IMIDAZOL-3-IUM-4-YL)-L-ALANINAMIDE'>0QS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUI:(3-AMINO-2,5-DIOXO-1-PYRROLIDINYL)ACETIC+ACID'>SUI</scene></td></tr>
-{{STRUCTURE_2jjj|  PDB=2jjj  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jjj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jjj OCA], [https://pdbe.org/2jjj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jjj RCSB], [https://www.ebi.ac.uk/pdbsum/2jjj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jjj 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/jj/2jjj_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=2jjj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Hydrogen atoms play key roles in enzyme mechanism, but as this study shows, even high-quality X-ray data to a resolution of 1 A cannot directly visualize them. Neutron diffraction, however, can locate deuterium atoms even at resolutions around 2 A. Both neutron and X-ray diffraction data have been used to investigate the transition state of the aspartic proteinase endothiapepsin. The different techniques reveal a different part of the story, revealing the clearest picture yet of the catalytic mechanism by which the enzyme operates. Room temperature neutron and X-ray diffraction data were used in a newly developed joint refinement software package to visualize deuterium atoms within the active site of the enzyme when a gem-diol transition state analogue inhibitor is bound at the active site. These data were also used to estimate their individual occupancy, while analysis of the differences between the bond lengths of the catalytic aspartates was performed using atomic resolution X-ray data. The two methods are in agreement on the protonation state of the active site with a transition state analogue inhibitor bound confirming the catalytic mechanism at which the enzyme operates.
-===ENDOTHIAPEPSIN IN COMPLEX WITH A GEM-DIOL INHIBITOR.===
+The catalytic mechanism of an aspartic proteinase explored with neutron and X-ray diffraction.,Coates L, Tuan HF, Tomanicek S, Kovalevsky A, Mustyakimov M, Erskine P, Cooper J J Am Chem Soc. 2008 Jun 11;130(23):7235-7. Epub 2008 May 15. PMID:18479128<ref>PMID:18479128</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2jjj" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18479128}}, adds the Publication Abstract to the page
+*[[Pepsin|Pepsin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18479128 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18479128}}
+__TOC__
+</StructureSection>
-==About this Structure==
-JJJ is a 1 chain structure of sequence 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=2JJJ OCA].
-==Reference==
-<ref group="xtra">PMID:18479128</ref><ref group="xtra">PMID:18084100</ref><references group="xtra"/>
 [[Category: Cryphonectria parasitica]]
-[[Category: Endothiapepsin]]
+[[Category: Large Structures]]
-[[Category: Coates, L.]]
+[[Category: Coates L]]
-[[Category: Cooper, J.]]
+[[Category: Cooper J]]
-[[Category: Erskine, P.]]
+[[Category: Erskine P]]
-[[Category: Kovalevsky, A.]]
+[[Category: Kovalevsky A]]
-[[Category: Mustyakimov, M.]]
+[[Category: Mustyakimov M]]
-[[Category: Tomanicek, S J.]]
+[[Category: Tomanicek SJ]]
-[[Category: Tuan, H F.]]
+[[Category: Tuan H-F]]
-[[Category: Acid proteinase]]
-[[Category: Aspartyl protease]]
-[[Category: Hydrolase inhibitor]]
-[[Category: Hydrolase/complex]]
-[[Category: Protease]]
-[[Category: Zymogen]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:26:23 2009''