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- PDB-2dca: X-ray crystal structure analysis of bovine spleen cathepsin B-CA0... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dca | ||||||
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Title | X-ray crystal structure analysis of bovine spleen cathepsin B-CA075 complex | ||||||
![]() | CATHEPSIN B | ||||||
![]() | HYDROLASE / Cathepsin B / Cysteine Protease / CA075 / EC 3.4.22.1 | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Watanabe, D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67 KB | Display | ![]() |
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PDB format | ![]() | 48 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 745.8 KB | Display | ![]() |
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Full document | ![]() | 753.2 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dc6C ![]() 2dc7C ![]() 2dc8C ![]() 2dc9C ![]() 2dcbC ![]() 2dccC ![]() 2dcdC ![]() 1itoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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) ![]() ![]() References: GenBank: 27806671, UniProt: P07688*PLUS, cathepsin B |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-75V / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.25 % |
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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: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 25, 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: 2.11→50 Å / Num. obs: 32750 / % possible obs: 99.5 % / Redundancy: 7.5 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 2.11→2.25 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.11 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure: ISOMORPHOUS REPLACEMENT Starting model: PDB ENTRY 1ITO Resolution: 2.11→9.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 343627.85 / 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: 59.0185 Å2 / ksol: 0.525691 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.11→9.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.24 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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