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- PDB-5d7a: Crystal structure of the kinase domain of TRAF2 and NCK-interacti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d7a | ||||||
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Title | Crystal structure of the kinase domain of TRAF2 and NCK-interacting protein kinase with NCB-0846 | ||||||
![]() | TRAF2 and NCK-interacting protein kinase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() microvillus assembly / regulation of dendrite morphogenesis / regulation of MAPK cascade / postsynaptic density, intracellular component / cytoskeleton organization / : / neuron projection morphogenesis / protein localization to plasma membrane / positive regulation of JNK cascade / recycling endosome ...microvillus assembly / regulation of dendrite morphogenesis / regulation of MAPK cascade / postsynaptic density, intracellular component / cytoskeleton organization / : / neuron projection morphogenesis / protein localization to plasma membrane / positive regulation of JNK cascade / recycling endosome / Wnt signaling pathway / MAPK cascade / presynapse / actin cytoskeleton organization / Oxidative Stress Induced Senescence / protein autophosphorylation / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of protein phosphorylation / apical plasma membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ohbayashi, N. / Kukimoto-Niino, M. / Yamada, T. / Shirouzu, M. | ||||||
![]() | ![]() Title: TNIK inhibition abrogates colorectal cancer stemness Authors: Masuda, M. / Uno, Y. / Ohbayashi, N. / Ohata, H. / Mimata, A. / Kukimoto-Niino, M. / Moriyama, H. / Kashimoto, S. / Inoue, T. / Goto, N. / Okamoto, K. / Shirouzu, M. / Sawa, M. / Yamada, 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 | ![]() | 183.4 KB | Display | ![]() |
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PDB format | ![]() | 146.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ax9C ![]() 5cwzC ![]() 2x7fS C: citing same article ( 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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35076.328 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9UKE5, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2M Ammonium sulfate 0.1M Bis-tris (5.6) 15% PEG3350 7% Ethyleneglycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→46.92 Å / Num. obs: 28803 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2X7F Resolution: 2.9→46.92 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→46.92 Å
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Refine LS restraints |
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LS refinement shell |
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