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- PDB-7ccu: Crystal structure of death-associated protein kinase 1 in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ccu | ||||||
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Title | Crystal structure of death-associated protein kinase 1 in complex with resveratrol | ||||||
![]() | Death-associated protein kinase 1 | ||||||
![]() | TRANSFERASE / protein kinase / inhibitor / complex / natural compound | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Yokoyama, T. / Suzuki, R. / Mizuguchi, M. | ||||||
![]() | ![]() Title: Crystal structure of death-associated protein kinase 1 in complex with the dietary compound resveratrol. Authors: Yokoyama, T. / Suzuki, R. / Mizuguchi, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.4 KB | Display | ![]() |
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PDB format | ![]() | 54 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 673.9 KB | Display | ![]() |
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Full document | ![]() | 674.8 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ccvC ![]() 7ccwC ![]() 5auxS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 33796.402 Da / Num. of mol.: 1 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-STL / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 35.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2.4 M ammonium sulfate, 0.1 M Tris-HCl pH 8.0, 14.4 mg/mL DAPK1, 2 mM resveratrol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.649→41.4 Å / Num. obs: 30997 / % possible obs: 97.3 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.649→1.71 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2999 / CC1/2: 0.881 / Rpim(I) all: 0.215 / Rrim(I) all: 0.578 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5AUX Resolution: 1.649→28.552 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.24 / 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: 1.649→28.552 Å
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Refine LS restraints |
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LS refinement shell |
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