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- PDB-3f5g: Crystal structure of death associated protein kinase in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f5g | ||||||
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Title | Crystal structure of death associated protein kinase in complex with ADP and Mg2+ | ||||||
![]() | Death-associated protein kinase 1 | ||||||
![]() | TRANSFERASE / kinase-ADP complex / Alternative splicing / ANK repeat / Apoptosis / ATP-binding / Calmodulin-binding / Cytoplasm / Kinase / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase | ||||||
Function / homology | ![]() cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / regulation of NMDA receptor activity / syntaxin-1 binding / calcium/calmodulin-dependent protein kinase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / regulation of NMDA receptor activity / syntaxin-1 binding / calcium/calmodulin-dependent protein kinase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / regulation of apoptotic process / protein autophosphorylation / postsynaptic density / negative regulation of translation / non-specific serine/threonine protein kinase / calmodulin binding / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / GTP binding / negative regulation of apoptotic process / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McNamara, L.K. / Watterson, D.M. / Brunzelle, J.S. | ||||||
![]() | ![]() Title: Structural insight into nucleotide recognition by human death-associated protein kinase. Authors: McNamara, L.K. / Watterson, D.M. / Brunzelle, J.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.2 KB | Display | ![]() |
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PDB format | ![]() | 57.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 755.4 KB | Display | ![]() |
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Full document | ![]() | 761.7 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3eh9C ![]() 3ehaC ![]() 3f5uC ![]() 1jksS S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 33794.367 Da / Num. of mol.: 1 Fragment: UNP residues 2-285, protein kinase domain,catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P53355, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.75 % |
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Crystal grow | Temperature: 295 K Details: 0.2 M ammonium chloride, 2.2 M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 2, 2008 / Details: BE LENSES |
Radiation | Monochromator: SINGLE DIAMOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 22396 / % possible obs: 98.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 4.15 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JKS Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.132 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.161 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.9 Å / Total num. of bins used: 20
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