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- PDB-3pwc: Bovine trypsin variant X(tripleGlu217Ile227) in complex with smal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pwc | ||||||
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Title | Bovine trypsin variant X(tripleGlu217Ile227) in complex with small molecule inhibitor | ||||||
![]() | Cationic trypsin | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / trypsin-like serine protease / hydrolase / protein binding / duodenum / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tziridis, A. / Neumann, P. / Kolenko, P. / Stubbs, M.T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.8 KB | Display | ![]() |
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PDB format | ![]() | 80.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 770.2 KB | Display | ![]() |
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Full document | ![]() | 771.3 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 22.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3plbC ![]() 3plkC ![]() 3plpC ![]() 3pm3C ![]() 3pmjC ![]() 3pwbC ![]() 3pyhC ![]() 3q00C ![]() 3unqC ![]() 3unsC ![]() 3uopC ![]() 3upeC ![]() 3uqoC ![]() 3uqvC ![]() 3uuzC ![]() 3uwiC ![]() 3uy9C ![]() 3v12C ![]() 3v13C ![]() 1v2kS 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23418.398 Da / Num. of mol.: 1 / Fragment: cationic trypsin, 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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 356 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ANH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ANH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / | ||||
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#3: Chemical | ChemComp-ANH / | ||||
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG8000, 0.2M 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: ![]() |
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: 1.6→30 Å / Num. all: 24403 / Num. obs: 24403 / % possible obs: 95.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 6 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1V2K Resolution: 1.6→28.8 Å / SU ML: 0.23 Isotropic thermal model: PROTEIN ANISOTROPIC, SOLVENT ISOTROPIC Cross valid method: THROUGHOUT / σ(F): 1.48 / 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: 37.865 Å2 / ksol: 0.328 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6→28.8 Å
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Refine LS restraints |
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LS refinement shell |
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