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1ito
From Proteopedia
| Line 5: | Line 5: | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=E6C:N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE'>E6C</scene> | |LIGAND= <scene name='pdbligand=E6C:N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE'>E6C</scene> | ||
| - | |ACTIVITY= [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] | + | |ACTIVITY= <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> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1dqd|1DQD]] | ||
| + | |RESOURCES=<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://www.ebi.ac.uk/pdbsum/1ito PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ito RCSB]</span> | ||
}} | }} | ||
| Line 31: | Line 34: | ||
[[Category: Tomoo, T.]] | [[Category: Tomoo, T.]] | ||
[[Category: Yamamoto, A.]] | [[Category: Yamamoto, A.]] | ||
| - | [[Category: E6C]] | ||
[[Category: cathepsin b]] | [[Category: cathepsin b]] | ||
[[Category: cysteine protease]] | [[Category: cysteine protease]] | ||
[[Category: e64c]] | [[Category: e64c]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:24:28 2008'' |
Revision as of 18:24, 30 March 2008
| |||||||
| , resolution 2.286Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Activity: | Cathepsin B, with EC number 3.4.22.1 | ||||||
| Related: | 1DQD
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure Analysis of Bovine Spleen Cathepsin B-E64c complex
Overview
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.
About this Structure
1ITO is a Single protein structure of sequence from Bos taurus. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Sun Mar 30 21:24:28 2008
Categories: Bos taurus | Cathepsin B | Single protein | Hara, T. | In, Y. | Ishida, T. | Kitamura, K. | Matsugi, K. | Murata, M. | Tomoo, T. | Yamamoto, A. | Cathepsin b | Cysteine protease | E64c
