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- PDB-3plk: Bovine trypsin variant X(tripleIle227) in complex with small mole... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3plk | ||||||
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Title | Bovine trypsin variant X(tripleIle227) 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. / Braeuer, U. / 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 | ![]() | 67.3 KB | Display | ![]() |
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PDB format | ![]() | 47 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 767.3 KB | Display | ![]() |
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Full document | ![]() | 769.8 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3plbC ![]() 3plpC ![]() 3pm3C ![]() 3pmjC ![]() 3pwbC ![]() 3pwcC ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23376.363 Da / Num. of mol.: 1 / Fragment: UNP residues 24-246 Mutation: N102E, L104Y, Y175S, P176S, G177F, Q178Y, S195A, V228I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 354 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 | ChemComp-SO4 / |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 8000, 0.1M imidazole, 0.1M ammonium sulphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. all: 28839 / Num. obs: 28839 / % possible obs: 98.6 % / Redundancy: 11.9 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 34 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1V2K Resolution: 1.53→47.3 Å / Cor.coef. Fo:Fc: 0.972 / SU B: 0.739 / SU ML: 0.028 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.672 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→47.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.568 Å / Total num. of bins used: 20
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