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Yorodumi- PDB-1bp4: USE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF CATHEP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bp4 | ||||||
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Title | USE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF CATHEPSIN K INHIBITORS. CRYSTAL STRUCTURES OF TWO PAPAIN INHIBITOR COMPLEXES DEMONSTRATE BINDING TO S'-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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lalonde, J.M. / Zhao, B. / Smith, W.W. / Janson, C.A. / Desjarlais, R.L. / Tomaszek, T.A. / Carr, T.J. / Thompson, S.K. / Yamashita, D.S. / Veber, D.F. / Abdel-Mequid, S.S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 1998 Title: Use of papain as a model for the structure-based design of cathepsin K inhibitors: crystal structures of two papain-inhibitor complexes demonstrate binding to S'-subsites. Authors: LaLonde, J.M. / Zhao, B. / Smith, W.W. / Janson, C.A. / DesJarlais, R.L. / Tomaszek, T.A. / Carr, T.J. / Thompson, S.K. / Oh, H.J. / Yamashita, D.S. / Veber, D.F. / Abdel-Meguid, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bp4.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bp4.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 1bp4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/1bp4 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/1bp4 | HTTPS FTP |
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-Related structure data
Related structure data | 1bqiC 1pipS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23449.346 Da / Num. of mol.: 1 / Fragment: NON / Source method: isolated from a natural source Details: ALDEHYDE INHIBITOR COVALENTLY BOUND TO ACTIVE SITE CYS 25 AS A HEMIMERCAPTAL. BOND OCCURS BETWEEN CYS 25-SG AND ALD 213-C22 Source: (natural) Carica papaya (papaya) / References: UniProt: P00784 |
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#2: Chemical | ChemComp-ALD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1995 |
Radiation | Monochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→10 Å / Num. obs: 14458 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.104 / Rsym value: 0.088 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.27 / % possible all: 60 |
Reflection | *PLUS Num. measured all: 62560 / Rmerge(I) obs: 0.0878 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PIP Resolution: 2.2→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2 Details: DISORDERED SIDE-CHAINS HAVE OCCUPANCIES SET TO ZERO IN COORDINATE FILE, RESIDUES 59,73,78,84,93,94,98,111,114,129,145
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Displacement parameters | Biso mean: 22.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 / Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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