+Open data
-Basic information
Entry | Database: PDB / ID: 2gcd | ||||||
---|---|---|---|---|---|---|---|
Title | TAO2 kinase domain-staurosporine structure | ||||||
Components | Serine/threonine-protein kinase TAO2 | ||||||
Keywords | TRANSFERASE / TAO2 / MAP3K / inhibitor / staurosporine | ||||||
Function / homology | Function and homology information basal dendrite morphogenesis / basal dendrite arborization / positive regulation of stress-activated MAPK cascade / neuropilin binding / focal adhesion assembly / regulation of postsynapse organization / mitogen-activated protein kinase kinase binding / regulation of synaptic membrane adhesion / mitotic G2 DNA damage checkpoint signaling / dendritic growth cone ...basal dendrite morphogenesis / basal dendrite arborization / positive regulation of stress-activated MAPK cascade / neuropilin binding / focal adhesion assembly / regulation of postsynapse organization / mitogen-activated protein kinase kinase binding / regulation of synaptic membrane adhesion / mitotic G2 DNA damage checkpoint signaling / dendritic growth cone / regulation of MAPK cascade / MAP kinase kinase kinase activity / stress-activated MAPK cascade / axonal growth cone / axonogenesis / neuron projection morphogenesis / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / cytoplasmic vesicle membrane / MAPK cascade / regulation of cell shape / cytoplasmic vesicle / actin cytoskeleton organization / postsynapse / positive regulation of MAPK cascade / cytoskeleton / receptor complex / non-specific serine/threonine protein kinase / neuron projection / axon / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / DNA damage response / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Zhou, T. / Sun, L. / Gao, Y. / Earnest, S. / Cobb, M.H. / Goldsmith, E.J. | ||||||
Citation | Journal: Acta Biochim.Biophys.Sinica / Year: 2006 Title: Crystal structure of the MAP3K TAO2 kinase domain bound by an inhibitor staurosporine. Authors: Zhou, T.J. / Sun, L.G. / Gao, Y. / Goldsmith, E.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2gcd.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2gcd.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 2gcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/2gcd ftp://data.pdbj.org/pub/pdb/validation_reports/gc/2gcd | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35436.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: tao2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9JLS3, EC: 2.7.1.37 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.1 % |
---|
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→25 Å / Num. obs: 31295 / % possible obs: 97.7 % / Rmerge(I) obs: 0.075 / Χ2: 1.022 / Net I/σ(I): 11 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→160.13 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.9 / SU B: 9.572 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.416 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 43.13 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→160.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.548→2.615 Å / Total num. of bins used: 20
|