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- PDB-2p7u: The crystal structure of rhodesain, the major cysteine protease o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2p7u | ||||||
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Title | The crystal structure of rhodesain, the major cysteine protease of T. brucei rhodesiense, bound to inhibitor K777 | ||||||
![]() | Cysteine protease | ||||||
![]() | HYDROLASE / cysteine protease / trypanosoma brucei / neglected disease | ||||||
Function / homology | ![]() proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Brinen, L.S. / Marion, R. | ||||||
![]() | ![]() Title: Vinyl sulfones as antiparasitic agents and a structural basis for drug design. Authors: Kerr, I.D. / Lee, J.H. / Farady, C.J. / Marion, R. / Rickert, M. / Sajid, M. / Pandey, K.C. / Caffrey, C.R. / Legac, J. / Hansell, E. / McKerrow, J.H. / Craik, C.S. / Rosenthal, P.J. / Brinen, L.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.9 KB | Display | ![]() |
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PDB format | ![]() | 41.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 775.6 KB | Display | ![]() |
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Full document | ![]() | 777.2 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2oz2C ![]() 3bwkC ![]() 1f2aS 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: 22903.188 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Species: Trypanosoma brucei / Strain: rhodesiense / Gene: rhodesain / Plasmid: pPIC Z / Production host: ![]() |
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#2: Chemical | ChemComp-D1R / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.14 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.0 M Sodium citrate; imidazole pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 15, 2000 / Details: MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. obs: 18751 / % possible obs: 89.7 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.047 |
Reflection shell | Resolution: 1.65→1.7 Å / Rmerge(I) obs: 0.147 / % possible all: 83.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1F2A WITHOUT INHIBITOR OR WATERS, WITH SIDE CHAINS THAT DIFFER CUT BACK TO ALANINE Resolution: 1.65→19.46 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.58 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→19.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.69 Å / Total num. of bins used: 20
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