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Yorodumi- PDB-2dcd: X-ray crystal structure analysis of bovine spleen cathepsin B-CA0... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dcd | ||||||
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Title | X-ray crystal structure analysis of bovine spleen cathepsin B-CA078 complex | ||||||
Components | CATHEPSIN B | ||||||
Keywords | HYDROLASE / Cathepsin B / Cysteine Protease / CA078 / EC 3.4.22.1 | ||||||
Function / homology | Function and homology information Trafficking and processing of endosomal TLR / Collagen degradation / cathepsin B / MHC class II antigen presentation / Neutrophil degranulation / proteolysis involved in protein catabolic process / melanosome / endopeptidase activity / lysosome / apical plasma membrane ...Trafficking and processing of endosomal TLR / Collagen degradation / cathepsin B / MHC class II antigen presentation / Neutrophil degranulation / proteolysis involved in protein catabolic process / melanosome / endopeptidase activity / lysosome / apical plasma membrane / cysteine-type endopeptidase activity / extracellular space Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / ISOMORPHOUS REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Watanabe, D. | ||||||
Citation | Journal: To be Published Title: Quantitative estimation of each active subsite of cathepsin B for the inhibitory activity, based on the inhibitory activitybinding mode relationship of a series of epoxysuccinyl inhibitors by ...Title: Quantitative estimation of each active subsite of cathepsin B for the inhibitory activity, based on the inhibitory activitybinding mode relationship of a series of epoxysuccinyl inhibitors by X-ray crystal structure analyses of the complexes Authors: Watanabe, D. / Yamamoto, A. / Matsumoto, K. / Murata, M. / Kitamura, K. / Tomoo, K. / Ishida, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dcd.cif.gz | 65.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dcd.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dcd_validation.pdf.gz | 702.9 KB | Display | wwPDB validaton report |
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Full document | 2dcd_full_validation.pdf.gz | 710.3 KB | Display | |
Data in XML | 2dcd_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 2dcd_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/2dcd ftp://data.pdbj.org/pub/pdb/validation_reports/dc/2dcd | HTTPS FTP |
-Related structure data
Related structure data | 2dc6C 2dc7C 2dc8C 2dc9C 2dcaC 2dcbC 2dccC 1itoS 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: 27919.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: SPLEEN References: GenBank: 27806671, UniProt: P07688*PLUS, cathepsin B |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-78A / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.4 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 50mM sodium citrate, 2.4M sodium phosphate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 17, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 13199 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.127 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 13.1 % / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS REPLACEMENT Starting model: PDB ENTRY 1ITO Resolution: 2.5→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1754260.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.6656 Å2 / ksol: 0.527378 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.65 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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