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Yorodumi- PDB-6fha: Death-associated Protein Kinase 1 (DAPK1) catalytic and auto-regu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fha | ||||||
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Title | Death-associated Protein Kinase 1 (DAPK1) catalytic and auto-regulatory domains with S289A and S308A mutations | ||||||
Components | Death-associated protein kinase 1 | ||||||
Keywords | SIGNALING PROTEIN / kinase / apoptosis / autophagy / CaMK | ||||||
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 / 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 / calmodulin binding / non-specific serine/threonine protein kinase / negative regulation of translation / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / GTP binding / apoptotic process / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Huart, A.-S. / Wilmanns, M. | ||||||
Citation | Journal: To Be Published Title: Molecular mechanisms behind DAPK regulation: how phosphorylation switches work Authors: Huart, A.-S. / Simon, B. / Lubner, J. / Mertens, H.D.T. / Temmerman, K. / Hoffmann, J.-E. / Svergun, D.I. / Schwartz, D. / Schultz, C. / Wilmanns, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fha.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fha.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 6fha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/6fha ftp://data.pdbj.org/pub/pdb/validation_reports/fh/6fha | HTTPS FTP |
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-Related structure data
Related structure data | 6fhbC 6qmoC 6qn4C 4b4lS 6fh9 S: Starting model for refinement 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: 38647.332 Da / Num. of mol.: 1 / Mutation: S289A S308A Source method: isolated from a genetically manipulated source Details: h / 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.4 % / Description: cuboid |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop Details: 22% PEG 4000, 0.2M ammonium sulfate, 0.1M sodium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2016 / Details: Toroidal mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.878→39.943 Å / Num. obs: 25549 / % possible obs: 91.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 35.977 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.067 / Rrim(I) all: 0.15 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.88→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.705 / Num. unique all: 992 / CC1/2: 0.018 / % possible all: 36.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4B4L Resolution: 2.3→39.943 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→39.943 Å
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Refine LS restraints |
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LS refinement shell |
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