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1ito

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(New page: 200px<br /><applet load="1ito" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ito, resolution 2.286&Aring;" /> '''Crystal Structure A...)
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[[Image:1ito.jpg|left|200px]]<br /><applet load="1ito" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ito, resolution 2.286&Aring;" />
 
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'''Crystal Structure Analysis of Bovine Spleen Cathepsin B-E64c complex'''<br />
 
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==Overview==
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==Crystal Structure Analysis of Bovine Spleen Cathepsin B-E64c complex==
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In order to elucidate the substrate specificity of the Sn subsites (n=1-3), of cathepsin B, its crystal structure inhibited by E64c, [(+)-(2S,3S)-3-(1-[N-(3-methylbutyl)amino]-leucylcarbonyl)oxirane-2-carbox, ylic acid] was analyzed by the X-ray diffraction method. Iterative manual, rebuilding and convenient conjugate refinement of structure decreased R-, and free R-factors to 19.7% and to 23.9%, respectively, where 130 water, molecules were included for the refinement using 14,759 independent, reflections from 10 to 2.3 A resolution. The epoxy carbonyl carbon of E64c, was covalently bonded to the Cys(29) S(gamma) atom and the remaining parts, were located at Sn subsites (n=1-3). The substrate specificity of these, subsites was characterized based on their interactions with the inhibitor., Base on these structural data, we developed a novel cathepsin B-specific, noncovalent-type inhibitor, which may bind to S2'-S3. The molecular design, of possessing structural elements of both CA074 and E64c, assisted by, energy minimization and molecular dynamics (MD) simulation, may lead to a, new lead noncovalent-type inhibitor.
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<StructureSection load='1ito' size='340' side='right'caption='[[1ito]], [[Resolution|resolution]] 2.29&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ito]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ITO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ITO FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.286&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E6C:N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE'>E6C</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ito FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ito OCA], [https://pdbe.org/1ito PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ito RCSB], [https://www.ebi.ac.uk/pdbsum/1ito PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ito ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/CATB_BOVIN CATB_BOVIN] Thiol protease which is believed to participate in intracellular degradation and turnover of proteins. Has also been implicated in tumor invasion and metastasis.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/it/1ito_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1ito ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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In order to elucidate the substrate specificity of the Sn subsites (n=1-3) of cathepsin B, its crystal structure inhibited by E64c [(+)-(2S,3S)-3-(1-[N-(3-methylbutyl)amino]-leucylcarbonyl)oxirane-2-carbox ylic acid] was analyzed by the X-ray diffraction method. Iterative manual rebuilding and convenient conjugate refinement of structure decreased R- and free R-factors to 19.7% and to 23.9%, respectively, where 130 water molecules were included for the refinement using 14,759 independent reflections from 10 to 2.3 A resolution. The epoxy carbonyl carbon of E64c was covalently bonded to the Cys(29) S(gamma) atom and the remaining parts were located at Sn subsites (n=1-3). The substrate specificity of these subsites was characterized based on their interactions with the inhibitor. Base on these structural data, we developed a novel cathepsin B-specific noncovalent-type inhibitor, which may bind to S2'-S3. The molecular design of possessing structural elements of both CA074 and E64c, assisted by energy minimization and molecular dynamics (MD) simulation, may lead to a new lead noncovalent-type inhibitor.
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==About this Structure==
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Structural basis for development of cathepsin B-specific noncovalent-type inhibitor: crystal structure of cathepsin B-E64c complex.,Yamamoto A, Tomoo K, Matsugi K, Hara T, In Y, Murata M, Kitamura K, Ishida T Biochim Biophys Acta. 2002 Jun 3;1597(2):244-51. PMID:12044902<ref>PMID:12044902</ref>
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1ITO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with E6C as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Cathepsin_B Cathepsin B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.1 3.4.22.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ITO OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structural basis for development of cathepsin B-specific noncovalent-type inhibitor: crystal structure of cathepsin B-E64c complex., Yamamoto A, Tomoo K, Matsugi K, Hara T, In Y, Murata M, Kitamura K, Ishida T, Biochim Biophys Acta. 2002 Jun 3;1597(2):244-51. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12044902 12044902]
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</div>
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[[Category: Bos taurus]]
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<div class="pdbe-citations 1ito" style="background-color:#fffaf0;"></div>
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[[Category: Cathepsin B]]
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[[Category: Single protein]]
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[[Category: Hara, T.]]
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[[Category: In, Y.]]
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[[Category: Ishida, T.]]
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[[Category: Kitamura, K.]]
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[[Category: Matsugi, K.]]
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[[Category: Murata, M.]]
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[[Category: Tomoo, T.]]
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[[Category: Yamamoto, A.]]
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[[Category: E6C]]
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[[Category: cathepsin b]]
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[[Category: cysteine protease]]
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[[Category: e64c]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:39:28 2007''
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==See Also==
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*[[Cathepsin 3D structures|Cathepsin 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Bos taurus]]
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[[Category: Large Structures]]
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[[Category: Hara T]]
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[[Category: In Y]]
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[[Category: Ishida T]]
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[[Category: Kitamura K]]
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[[Category: Matsugi K]]
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[[Category: Murata M]]
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[[Category: Tomoo T]]
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[[Category: Yamamoto A]]

Current revision

Crystal Structure Analysis of Bovine Spleen Cathepsin B-E64c complex

PDB ID 1ito

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