[English] 日本語
![](img/lk-miru.gif)
- PDB-3uqo: Bovine trypsin variant X(triplePhe227) in complex with small mole... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3uqo | ||||||
---|---|---|---|---|---|---|---|
Title | Bovine trypsin variant X(triplePhe227) 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 62.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 43.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 753.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 754.7 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3plbC ![]() 3plkC ![]() 3plpC ![]() 3pm3C ![]() 3pmjC ![]() 3pwbC ![]() 3pwcC ![]() 3pyhC ![]() 3q00C ![]() 3unqC ![]() 3unsC ![]() 3uopC ![]() 3upeC ![]() 3uqvC ![]() 3uuzC ![]() 3uwiC ![]() 3uy9C ![]() 3v12C ![]() 3v13C ![]() 1v2kS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 23410.379 Da / Num. of mol.: 1 Mutation: N102E, L104Y, Y175S, P176S, G177F, Q178Y, S195A, V228F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-3YH / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.95 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG8000, 0.1M AMMONIUM SULPHATE, 0.1M IMIDAZOLE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 18782 / Num. obs: 18782 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 5.7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.1 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1V2K Resolution: 1.8→30 Å / SU ML: 0.22 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 14.84 / Stereochemistry target values: ML
| |||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.67 Å2 / ksol: 0.334 e/Å3 | |||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|