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Yorodumi- PDB-1ppp: CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ppp | ||||||
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Title | CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING DIVERSITY OF E64-C TO PAPAIN S2 AND S3 SUBSITES | ||||||
Components | PAPAIN | ||||||
Keywords | HYDROLASE(SULFHYDRYL PROTEINASE) | ||||||
Function / homology | Function and homology information papain / serpin family protein binding / cysteine-type peptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | Carica papaya (papaya) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Ishida, T. | ||||||
Citation | Journal: Biochem.J. / Year: 1992 Title: Crystal structure of papain-E64-c complex. Binding diversity of E64-c to papain S2 and S3 subsites. Authors: Kim, M.J. / Yamamoto, D. / Matsumoto, K. / Inoue, M. / Ishida, T. / Mizuno, H. / Sumiya, S. / Kitamura, K. #1: Journal: J.Biol.Chem. / Year: 1991 Title: Refined X-Ray Structure of Papain(Dot)E-64-C Complex at 2.1-Angstroms Resolution Authors: Yamamoto, D. / Matsumoto, K. / Ohishi, H. / Ishida, T. / Inoue, M. / Kitamura, K. / Mizuno, H. #2: Journal: FEBS Lett. / Year: 1989 Title: Mode of Binding of E-64-C, a Potent Thiol Protease Inhibitor, to Papain as Determined by X-Ray Crystal Analysis of the Complex Authors: Matsumoto, K. / Yamamoto, D. / Ohishi, H. / Tomoo, K. / Ishida, T. / Inoue, M. / Sadatome, T. / Kitamura, K. / Mizuno, H. #3: Journal: FEBS Lett. / Year: 1990 Title: The Importance of Val-157 Hydrophobic Interaction for Papain Inhibitory Activity of an Epoxysuccinyl Amino Acid Derivative; a Structure-Activity Relationship Based on the Crystal Structure of ...Title: The Importance of Val-157 Hydrophobic Interaction for Papain Inhibitory Activity of an Epoxysuccinyl Amino Acid Derivative; a Structure-Activity Relationship Based on the Crystal Structure of the Papain-E-64-C Complex Authors: Yamamoto, D. / Matsumoto, K. / Ohishi, H. / Ishida, T. / Inoue, M. / Kitamura, K. / Mizuno, H. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 4, 5, 6 OF S1A ARE IDENTICAL TO STRANDS 2, 3, 4 OF SHEET S1B. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ppp.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ppp.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ppp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/1ppp ftp://data.pdbj.org/pub/pdb/validation_reports/pp/1ppp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 152 2: THE BOND BETWEEN ATOMS O1 AND C2 IS BROKEN WHEN E-64-C BINDS TO PAPAIN IN THIS STRUCTURE. |
-Components
#1: Protein | Mass: 23449.346 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carica papaya (papaya) / References: UniProt: P00784, papain |
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#2: Chemical | ChemComp-E6C / |
#3: Chemical | ChemComp-MOH / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | E6C IS (2S,3S)-3-(1-(N-(3-METHYLBUTYL)AMINO)- LEUCYLCARBOXYL)OXIRANE-2-CARBOXYLATE. THIS COMPOUND ...E6C IS (2S,3S)-3-(1-(N-(3-METHYLBUTY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.94 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 9.2 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 14811 / Observed criterion σ(F): 3 / Num. measured all: 21135 / Rmerge(I) obs: 0.087 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.194 / Highest resolution: 1.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. reflection obs: 14811 / Rfactor obs: 0.194 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |