[English] 日本語
Yorodumi- PDB-3pwc: Bovine trypsin variant X(tripleGlu217Ile227) in complex with smal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pwc | ||||||
---|---|---|---|---|---|---|---|
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 cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3pwc.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3pwc.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 3pwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pwc_validation.pdf.gz | 770.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3pwc_full_validation.pdf.gz | 771.3 KB | Display | |
Data in XML | 3pwc_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 3pwc_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/3pwc ftp://data.pdbj.org/pub/pdb/validation_reports/pw/3pwc | 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 (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-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.) Bos taurus (cattle) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin |
---|
-Non-polymers , 5 types, 356 molecules
#2: Chemical | ChemComp-CA / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-ANH / | ||||
#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.29 % |
---|---|
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 |
---|---|
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: 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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→28.8 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|