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1ito

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Revision as of 08:51, 17 January 2018

Crystal Structure Analysis of Bovine Spleen Cathepsin B-E64c complex

Structural highlights

1ito is a 1 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1dqd
Activity:	Cathepsin B, with EC number 3.4.22.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Yamamoto A, Tomoo K, Matsugi K, Hara T, In Y, Murata M, Kitamura K, Ishida T. Structural basis for development of cathepsin B-specific noncovalent-type inhibitor: crystal structure of cathepsin B-E64c complex. Biochim Biophys Acta. 2002 Jun 3;1597(2):244-51. PMID:12044902

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ito"

@@ Line 1: / Line 1: @@
 ==Crystal Structure Analysis of Bovine Spleen Cathepsin B-E64c complex==
 <StructureSection load='1ito' size='340' side='right' caption='[[1ito]], [[Resolution|resolution]] 2.29&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dqd|1dqd]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=1ito FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ito OCA], [http://pdbe.org/1ito PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ito RCSB], [http://www.ebi.ac.uk/pdbsum/1ito PDBsum]</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=1ito FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ito OCA], [http://pdbe.org/1ito PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ito RCSB], [http://www.ebi.ac.uk/pdbsum/1ito PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ito ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/it/1ito_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/it/1ito_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 30: @@
 </div>
 <div class="pdbe-citations 1ito" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Cathepsin|Cathepsin]]
 == References ==
 <references/>

1ito

From Proteopedia

Revision as of 08:51, 17 January 2018

Crystal Structure Analysis of Bovine Spleen Cathepsin B-E64c complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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