3h89: Difference between revisions

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-[[Image:3h89.png|left|200px]]
-<!--
+==A combined crystallographic and molecular dynamics study of cathepsin-L retro-binding inhibitors(compound 4)==
-The line below this paragraph, containing "STRUCTURE_3h89", creates the "Structure Box" on the page.
+<StructureSection load='3h89' size='340' side='right'caption='[[3h89]], [[Resolution|resolution]] 2.50&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'>[[3h89]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H89 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3H89 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NSX:N~2~,N~6~-BIS(BIPHENYL-4-YLACETYL)-L-LYSYL-D-ARGINYL-N-(2-PHENYLETHYL)-L-TYROSINAMIDE'>NSX</scene></td></tr>
--->
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3h8b|3h8b]], [[3h8c|3h8c]]</div></td></tr>
-{{STRUCTURE_3h89|  PDB=3h89  |  SCENE=  }}
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Catehpsin L ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cathepsin_L Cathepsin L], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.15 3.4.22.15] </span></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=3h89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h89 OCA], [https://pdbe.org/3h89 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3h89 RCSB], [https://www.ebi.ac.uk/pdbsum/3h89 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3h89 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/CATL1_HUMAN CATL1_HUMAN]] Important for the overall degradation of proteins in lysosomes.
+== 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/h8/3h89_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=3h89 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We report the crystal structures of three noncovalent retrobinding inhibitors in complex with mature cathepsin L up to resolutions of 2.5, 1.8, and 2.5 A, respectively. These inhibitors were Bpa-(Nepsilon-Bpa)Lys-DArg-Tyr-Npe, Bpa-(Nepsilon-Bpa)Lys-DArg-Phe-Npe, and Bpa-MCys-DArg-Phe-Npe, where Bpa = biphenylacetyl and Pea = N-phenylethyl. These were selected to clarify the binding mode of the biphenyl groups in the S' subsites because the addition of a second biphenyl does not improve potency. Examination of the symmetry-related monomers in the crystal structures revealed inhibitor-inhibitor crystal packing interactions. Molecular dynamics simulations were then used to explore the structure and dynamical behavior of the isolated protein-ligand complexes in solution. In the simulations, the backbone biphenyl groups for all three inhibitors ended up in the same location despite having started out in different orientations in the initial crystal structure conformations. The lack of improved potency of the larger inhibitors over the smaller one is attributed to a correspondingly greater entropic cost of binding.
-===A combined crystallographic and molecular dynamics study of cathepsin-L retro-binding inhibitors(compound 4)===
+A combined crystallographic and molecular dynamics study of cathepsin L retrobinding inhibitors.,Shenoy RT, Chowdhury SF, Kumar S, Joseph L, Purisima EO, Sivaraman J J Med Chem. 2009 Oct 22;52(20):6335-46. PMID:19761244<ref>PMID:19761244</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_19761244}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3h89" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19761244 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_19761244}}
-==About this Structure==
-[[3h89]] is a 6 chain structure of [[Cathepsin]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H89 OCA].
 ==See Also==
-*[[Cathepsin]]
+*[[Cathepsin 3D structures|Cathepsin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:19761244</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Cathepsin L]]
-[[Category: Homo sapiens]]
+[[Category: Human]]
-[[Category: Chowdhury, S F.]]
+[[Category: Large Structures]]
-[[Category: Joseph, L.]]
+[[Category: Chowdhury, S F]]
-[[Category: Kumar, S.]]
+[[Category: Joseph, L]]
-[[Category: Purisima, E O.]]
+[[Category: Kumar, S]]
-[[Category: Sivaraman, J.]]
+[[Category: Purisima, E O]]
-[[Category: Tulsidas, S R.]]
+[[Category: Sivaraman, J]]
+[[Category: Tulsidas, S R]]
 [[Category: Cathepsin l]]
 [[Category: Cysteine protease]]