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- PDB-4ypd: Crystal Structure of DAPK1 catalytic domain in complex with the h... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ypd | ||||||
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Title | Crystal Structure of DAPK1 catalytic domain in complex with the hinge binding fragment 4-methylpyridazine | ||||||
![]() | Death-associated protein kinase 1 | ||||||
![]() | TRANSFERASE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Grum-Tokars, V.L. / Minasov, G. / Roy, S.M. / Anderson, W.F. / Watterson, D.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of DAPK1 catalytic domain in complex with hinge binding fragments Authors: Grum-Tokars, V.L. / Minasov, G. / Roy, S.M. / Anderson, W.F. / Watterson, D.M. #1: ![]() Title: Development of Novel In Vivo Chemical Probes to Address CNS Protein Kinase Involvement in Synaptic Dysfunction. Authors: Watterson, D.M. / Grum-Tokars, V.L. / Roy, S.M. / Schavocky, J.P. / Bradaric, B.D. / Bachstetter, A.D. / Xing, B. / Dimayuga, E. / Saeed, F. / Zhang, H. / Staniszewski, A. / Pelletier, J.C. ...Authors: Watterson, D.M. / Grum-Tokars, V.L. / Roy, S.M. / Schavocky, J.P. / Bradaric, B.D. / Bachstetter, A.D. / Xing, B. / Dimayuga, E. / Saeed, F. / Zhang, H. / Staniszewski, A. / Pelletier, J.C. / Minasov, G. / Anderson, W.F. / Arancio, O. / Van Eldik, L.J. #2: Journal: Biochim.Biophys.Acta / Year: 2011 Title: Site-directed mutagenesis of the glycine-rich loop of death associated protein kinase (DAPK) identifies it as a key structure for catalytic activity. Authors: McNamara, L.K. / Brunzelle, J.S. / Schavocky, J.P. / Watterson, D.M. / Grum-Tokars, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.2 KB | Display | ![]() |
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PDB format | ![]() | 113.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.2 KB | Display | ![]() |
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Full document | ![]() | 461.4 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yo4C ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 33794.367 Da / Num. of mol.: 1 / Fragment: protein kinase domain (UNP residues 2-285) 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-CL / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-DKG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.63 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 1.7 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2011 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. obs: 57841 / % possible obs: 99.5 % / Redundancy: 7.2 % / Net I/σ(I): 23.33 |
Reflection shell | Highest resolution: 1.35 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1JKS Resolution: 1.4→29.46 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.903 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.32 Å2 / Biso mean: 24.216 Å2 / Biso min: 12.09 Å2
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Refinement step | Cycle: final / Resolution: 1.4→29.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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