1pe6
From Proteopedia
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|PDB= 1pe6 |SIZE=350|CAPTION= <scene name='initialview01'>1pe6</scene>, resolution 2.1Å | |PDB= 1pe6 |SIZE=350|CAPTION= <scene name='initialview01'>1pe6</scene>, resolution 2.1Å | ||
|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>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.22.2 4.3.22.2] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Lyase Lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.22.2 4.3.22.2] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pe6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pe6 OCA], [http://www.ebi.ac.uk/pdbsum/1pe6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pe6 RCSB]</span> | ||
}} | }} | ||
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[[Category: Ohishi, H.]] | [[Category: Ohishi, H.]] | ||
[[Category: Yamamoto, D.]] | [[Category: Yamamoto, D.]] | ||
| - | [[Category: E6C]] | ||
| - | [[Category: MOH]] | ||
[[Category: hydrolase (sulfhydryl proteinase)]] | [[Category: hydrolase (sulfhydryl proteinase)]] | ||
| - | ''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 22:58:28 2008'' |
Revision as of 19:58, 30 March 2008
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| , resolution 2.1Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Activity: | Lyase, with EC number 4.3.22.2 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
REFINED X-RAY STRUCTURE OF PAPAIN(DOT)E-64-C COMPLEX AT 2.1-ANGSTROMS RESOLUTION
Overview
E-64-c, a synthetic cysteine protease inhibitor designed from E-64, binds to papain through a thioether covalent bond. The x-ray diffraction data for 2.1-A resolution were used to determine the three-dimensional structure of this complex and refined it to R = 0.159. 0.159. In the complex structure, the configurational conversion from S to R took place on the epoxy carbon of E-64-c, implying that the nucleophilic attack of the Cys-25 thiol group occurs at the opposite side of the epoxy oxygen atom. The leucyl and isoamylamide groups of E-64-c were strongly fixed to papain S subsites by specific interactions, including hydrogen bonding to the Gly-66 residue. The carboxyl-terminal anion of E-64-c formed an electrostatic interaction with the protonated His-159 imidazole ring (O-...HN+ = 3.76 A) and consequently prevented the participation of this residue in the hydrolytic charge-relay system. No significant distortion caused by the binding of E-64-c was shown in the secondary structure of papain. It is important to note that inhibitor and substrate have opposite binding modes for the peptide groups. The possible relationship between the binding mode and inhibitory activity is discussed on the basis of the crystal structure of this complex.
About this Structure
1PE6 is a Single protein structure of sequence from [1]. Full crystallographic information is available from OCA.
Reference
Refined x-ray structure of papain.E-64-c complex at 2.1-A resolution., Yamamoto D, Matsumoto K, Ohishi H, Ishida T, Inoue M, Kitamura K, Mizuno H, J Biol Chem. 1991 Aug 5;266(22):14771-7. PMID:1860874
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