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- PDB-2jed: The crystal structure of the kinase domain of the protein kinase ... -
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Basic information
Entry | Database: PDB / ID: 2jed | ||||||
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Title | The crystal structure of the kinase domain of the protein kinase C theta in complex with NVP-XAA228 at 2.32A resolution. | ||||||
![]() | PROTEIN KINASE C THETA | ||||||
![]() | TRANSFERASE / PHOSPHORYLATION / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / POLYMORPHISM / METAL-BINDING / ZINC / KINASE / PKC THETA / MAGNESIUM / ZINC-FINGER / ALTERNATIVE SPLICING / PHORBOL-ESTER BINDING | ||||||
Function / homology | ![]() positive regulation of T-helper 2 cell activation / protein kinase C / Netrin-1 signaling / diacylglycerol-dependent serine/threonine kinase activity / Effects of PIP2 hydrolysis / regulation of platelet aggregation / CD4-positive, alpha-beta T cell proliferation / positive regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of T cell apoptotic process / positive regulation of T-helper 17 type immune response ...positive regulation of T-helper 2 cell activation / protein kinase C / Netrin-1 signaling / diacylglycerol-dependent serine/threonine kinase activity / Effects of PIP2 hydrolysis / regulation of platelet aggregation / CD4-positive, alpha-beta T cell proliferation / positive regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of T cell apoptotic process / positive regulation of T-helper 17 type immune response / aggresome / positive regulation of interleukin-4 production / Apoptotic cleavage of cellular proteins / positive regulation of interleukin-17 production / Fc-epsilon receptor signaling pathway / positive regulation of telomere capping / membrane protein ectodomain proteolysis / immunological synapse / centriolar satellite / : / positive regulation of telomere maintenance via telomerase / positive regulation of interleukin-2 production / negative regulation of insulin receptor signaling pathway / cell chemotaxis / regulation of cell growth / axon guidance / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / FCERI mediated NF-kB activation / G alpha (z) signalling events / RAS processing / Inactivation, recovery and regulation of the phototransduction cascade / Downstream TCR signaling / positive regulation of T cell activation / positive regulation of NF-kappaB transcription factor activity / protein kinase activity / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / ATP binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stark, W. / Bitsch, F. / Berner, A. / Buelens, F. / Graff, P. / Depersin, H. / Geiser, M. / Knecht, R. / Rahuel, J. / Rummel, G. ...Stark, W. / Bitsch, F. / Berner, A. / Buelens, F. / Graff, P. / Depersin, H. / Geiser, M. / Knecht, R. / Rahuel, J. / Rummel, G. / Schlaeppi, J.M. / Schmitz, R. / Strauss, A. / Wagner, J. | ||||||
![]() | ![]() Title: The Crystal Structure of the Kinase Domain of the Protein Kinase C Theta in Complex with Nvp-Xaa228 Authors: Stark, W. / Bitsch, F. / Berner, A. / Buelens, F. / Graff, P. / Depersin, H. / Fendrich, G. / Geiser, M. / Knecht, R. / Rahuel, J. / Rummel, G. / Schlaeppi, J.M. / Schmitz, R. / Strauss, A. / Wagner, J. #1: Journal: Protein Expression Purif. / Year: 2007 Title: Improved Expression of Kinases in Baculovirus-Infected Insect Cells Upon Addition of Specific Kinase Inhibitors to the Culture Helpful for Structural Studies. Authors: Strauss, A. / Fendrich, G. / Horisberger, M.A. / Liebetanz, J. / Meyhack, B. / Schlaeppi, J.-M. / Schmitz, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157 KB | Display | ![]() |
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PDB format | ![]() | 123 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 32 KB | Display | |
Data in CIF | ![]() | 45 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1fotS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41823.965 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN 361-706 / Mutation: YES / Source method: isolated from a natural source Details: PHOSPHOSERINE 676, PHOSPHOSERINE 695, C540 MODIFIED Source: (natural) ![]() #2: Chemical | #3: Chemical | ChemComp-MPD / ( | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ILE 381 TO GLU ENGINEERED RESIDUE IN CHAIN A, THR 538 TO GLU ...ENGINEERED | Sequence details | MUTATIONS I381E, T538E | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 Details: VAPOR DIFFUSION AT 4C PROTEIN SOLUTION: 10MG/ML PROTEIN IN 0.2M NACL, 0.05M IMIDAZOLE, 0.001M NAF, 0.05M TCEP, PH = 8.0 RESERVOIR SOLUTION: 0.1 M NA-CACODYLATE PH = 6.5 24% MPD (V/V) 4% ...Details: VAPOR DIFFUSION AT 4C PROTEIN SOLUTION: 10MG/ML PROTEIN IN 0.2M NACL, 0.05M IMIDAZOLE, 0.001M NAF, 0.05M TCEP, PH = 8.0 RESERVOIR SOLUTION: 0.1 M NA-CACODYLATE PH = 6.5 24% MPD (V/V) 4% PEG8000 (W/V) DROP: 1:1 SMALL ORGANIC MOLECULES LIKE 2,5-HEXANEDIOL AND SULFOBETAINE-195 HAVE A POSITIVE EFFECT ON THE CRYSTAL GROWTH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 6, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918396 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→50 Å / Num. obs: 42831 / % possible obs: 99.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.32→2.36 Å / Rmerge(I) obs: 0.48 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FOT Resolution: 2.32→19.88 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.404 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.198 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→19.88 Å
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Refine LS restraints |
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