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Open data
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Basic information
Entry | Database: PDB / ID: 5aut | ||||||
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Title | Crystal structure of DAPK1 in complex with ANS. | ||||||
![]() | Death-associated protein kinase 1 | ||||||
![]() | TRANSFERASE / death-associated protein kinase 1 / serin/threonine protein kinase / complex | ||||||
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. / Mizuguchi, M. / Kosaka, Y. | ||||||
![]() | ![]() Title: Structural Insight into the Interactions between Death-Associated Protein Kinase 1 and Natural Flavonoids. Authors: Yokoyama, T. / Kosaka, Y. / 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 | ![]() | 75.1 KB | Display | ![]() |
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PDB format | ![]() | 53.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 804 KB | Display | ![]() |
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Full document | ![]() | 806.9 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5auuC ![]() 5auvC ![]() 5auwC ![]() 5auxC ![]() 5auyC ![]() 5auzC ![]() 5av0C ![]() 5av1C ![]() 5av2C ![]() 5av3C ![]() 5av4C ![]() 1jksS 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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Unit cell |
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Components
#1: Protein | Mass: 33796.402 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-285 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-2AN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 2 M ammonium sulfate, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→44.3 Å / Num. obs: 28573 / % possible obs: 97.6 % / Redundancy: 4.4 % / Net I/σ(I): 31.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JKS Resolution: 1.7→34.453 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 17.96 / 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: 1.7→34.453 Å
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Refine LS restraints |
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LS refinement shell |
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