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Yorodumi- PDB-5av4: Crystal structure of DAPK1-genistein complex in the presence of b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5av4 | ||||||
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Title | Crystal structure of DAPK1-genistein complex in the presence of bromide ions. | ||||||
Components | Death-associated protein kinase 1DAPK1 | ||||||
Keywords | TRANSFERASE / death-associated protein kinase 1 / serine/threonine protein kinase / natural flavonoid | ||||||
Function / homology | Function and homology information 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 / syntaxin-1 binding / regulation of NMDA receptor activity / 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 / syntaxin-1 binding / regulation of NMDA receptor activity / 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 / calmodulin binding / non-specific serine/threonine protein kinase / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å | ||||||
Authors | Yokoyama, T. / Mizuguchi, M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5av4.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5av4.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 5av4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/5av4 ftp://data.pdbj.org/pub/pdb/validation_reports/av/5av4 | HTTPS FTP |
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-Related structure data
Related structure data | 5autC 5auuC 5auvC 5auwC 5auxC 5auyC 5auzC 5av0C 5av1C 5av2C 5av3C C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: DAPK1, DAPK / Production host: Escherichia coli (E. coli) References: UniProt: P53355, non-specific serine/threonine protein kinase | ||
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#2: Chemical | ChemComp-GEN / | ||
#3: Chemical | ChemComp-BR / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2 M ammonium sulfate, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.90681 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.90681 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→28.6 Å / Num. obs: 50233 / % possible obs: 96.8 % / Redundancy: 7.2 % / Net I/σ(I): 24.3 |
-Processing
Software |
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Refinement | Resolution: 1.4→28.579 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 22.29 / 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: 1.4→28.579 Å
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Refine LS restraints |
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LS refinement shell |
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