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Yorodumi- PDB-3pyh: Bovine trypsin variant X(tripleGlu217Ile227) in complex with smal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pyh | ||||||
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Title | Bovine trypsin variant X(tripleGlu217Ile227) in complex with small molecule inhibitor | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Trypsin-like serine protease / HYDROLASE / PROTEIN BINDING / DUODENUM / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Tziridis, A. / Neumann, P. / Kolenko, P. / Stubbs, M.T. | ||||||
Citation | Journal: Biol.Chem. / Year: 2014 Title: Correlating structure and ligand affinity in drug discovery: a cautionary tale involving second shell residues. Authors: Tziridis, A. / Rauh, D. / Neumann, P. / Kolenko, P. / Menzel, A. / Brauer, U. / Ursel, C. / Steinmetzer, P. / Sturzebecher, J. / Schweinitz, A. / Steinmetzer, T. / Stubbs, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pyh.cif.gz | 65 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pyh.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/3pyh ftp://data.pdbj.org/pub/pdb/validation_reports/py/3pyh | HTTPS FTP |
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-Related structure data
Related structure data | 3plbC 3plkC 3plpC 3pm3C 3pmjC 3pwbC 3pwcC 3q00C 3unqC 3unsC 3uopC 3upeC 3uqoC 3uqvC 3uuzC 3uwiC 3uy9C 3v12C 3v13C 1v2kS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23418.398 Da / Num. of mol.: 1 / Fragment: UNP residues 24-246 Mutation: N102E, L104Y, Y175S, P176S, G177F, Q178I, S195A, S118E, V228I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin |
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-Non-polymers , 5 types, 268 molecules
#2: Chemical | ChemComp-CA / |
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#3: Chemical | ChemComp-3YH / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-CL / |
#6: 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: 2.61 Å3/Da / Density % sol: 52.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% PEG8000,0.1M AMMONIUM SULPHATE, 0.1M IMIDAZOLE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 16366 / Num. obs: 16366 / % possible obs: 99.9 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V2K Resolution: 2→19.619 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.355 Å2 / ksol: 0.397 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→19.619 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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