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- PDB-5a6o: Crystal structure of the apo form of the unphosphorylated human d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a6o | ||||||
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Title | Crystal structure of the apo form of the unphosphorylated human death associated protein kinase 3 (DAPK3) | ||||||
![]() | DEATH-ASSOCIATED PROTEIN KINASE 3 | ||||||
![]() | TRANSFERASE / DAPK3 / APO / DEATH-ASSOCIATED PROTEIN KINASE 3 / ZIPPER-INTERACTING PROTEIN KINASE | ||||||
Function / homology | ![]() regulation of myosin II filament organization / leucine zipper domain binding / cAMP response element binding protein binding / regulation of smooth muscle contraction / Caspase activation via Dependence Receptors in the absence of ligand / regulation of cell motility / regulation of focal adhesion assembly / regulation of mitotic nuclear division / regulation of mitotic cell cycle / regulation of autophagy ...regulation of myosin II filament organization / leucine zipper domain binding / cAMP response element binding protein binding / regulation of smooth muscle contraction / Caspase activation via Dependence Receptors in the absence of ligand / regulation of cell motility / regulation of focal adhesion assembly / regulation of mitotic nuclear division / regulation of mitotic cell cycle / regulation of autophagy / regulation of actin cytoskeleton organization / apoptotic signaling pathway / PML body / small GTPase binding / cellular response to type II interferon / positive regulation of canonical Wnt signaling pathway / chromatin organization / regulation of cell shape / regulation of apoptotic process / protein autophosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / intracellular signal transduction / positive regulation of cell migration / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / regulation of DNA-templated transcription / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rodrigues, T. / Reker, D. / Welin, M. / Caldera, M. / Brunner, C. / Gabernet, G. / Schneider, P. / Walse, B. / Schneider, G. | ||||||
![]() | ![]() Title: De Novo Fragment Design for Drug Discovery and Chemical Biology. Authors: Rodrigues, T. / Reker, D. / Welin, M. / Caldera, M. / Brunner, C. / Gabernet, G. / Schneider, P. / Walse, B. / Schneider, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.4 KB | Display | ![]() |
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PDB format | ![]() | 98.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.7 KB | Display | ![]() |
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Full document | ![]() | 459.5 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a6nC ![]() 3hby 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.998, 0.052, -0.042), Vector: |
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Components
#1: Protein | Mass: 32545.123 Da / Num. of mol.: 2 / Fragment: PROTEIN KINASE DOMAIN, UNP RESIDUES 9-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O43293, 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: 2.46 Å3/Da / Density % sol: 50.01 % / Description: NONE |
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Crystal grow | pH: 6.2 Details: 23% PROPANEDIOL, 0.1M NA/K PHOSPHATE PH 6.2, 10% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2015 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06883 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→29.32 Å / Num. obs: 85030 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3HBY ![]() 3hby Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.905 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 170-174 ARE DISORDERED
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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: 23.894 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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