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- PDB-2yak: Structure of death-associated protein Kinase 1 (dapk1) in complex... -
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Basic information
Entry | Database: PDB / ID: 2yak | ||||||
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Title | Structure of death-associated protein Kinase 1 (dapk1) in complex with a ruthenium octasporine ligand (OSV) | ||||||
![]() | DEATH-ASSOCIATED PROTEIN KINASE 1 | ||||||
![]() | TRANSFERASE / OCTAHEDRAL RUTHENIUM INHIBITORY COMPLEX / KINASE INHIBITOR | ||||||
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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Feng, L. / Geisselbrecht, Y. / Blanck, S. / Wilbuer, A. / Atilla-Gokcumen, G.E. / Filippakopoulos, P. / Kraeling, K. / Celik, M.A. / Harms, K. / Maksimoska, J. ...Feng, L. / Geisselbrecht, Y. / Blanck, S. / Wilbuer, A. / Atilla-Gokcumen, G.E. / Filippakopoulos, P. / Kraeling, K. / Celik, M.A. / Harms, K. / Maksimoska, J. / Marmorstein, R. / Frenking, G. / Knapp, S. / Essen, L.-O. / Meggers, E. | ||||||
![]() | ![]() Title: Structurally Sophisticated Octahedral Metal Complexes as Highly Selective Protein Kinase Inhibitors. Authors: Feng, L. / Geisselbrecht, Y. / Blanck, S. / Wilbuer, A. / Atilla-Gokcumen, G.E. / Filippakopoulos, P. / Kraeling, K. / Celik, M.A. / Harms, K. / Maksimoska, J. / Marmorstein, R. / Frenking, ...Authors: Feng, L. / Geisselbrecht, Y. / Blanck, S. / Wilbuer, A. / Atilla-Gokcumen, G.E. / Filippakopoulos, P. / Kraeling, K. / Celik, M.A. / Harms, K. / Maksimoska, J. / Marmorstein, R. / Frenking, G. / Knapp, S. / Essen, L.O. / Meggers, E. #1: ![]() Title: Targeting Large Kinase Active Site with Rigid, Bulky Octahedral Ruthenium Complexes. Authors: Maksimoska, J. / Feng, L. / Harms, K. / Yi, C. / Kissil, J. / Marmorstein, R. / Meggers, E. #2: ![]() Title: Extremely Tight Binding of a Ruthenium Complex to Glycogen Synthase Kinase 3. Authors: Atilla-Gokcumen, G.E. / Pagano, N. / Streu, C. / Maksimoska, J. / Filippakopoulos, P. / Knapp, S. / Meggers, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 129.5 KB | Display | ![]() |
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PDB format | ![]() | 101.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: 32725.262 Da / Num. of mol.: 1 / Fragment: AA, 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-OSV / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.11 % |
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Crystal grow | Details: 100 MM TRIS PH 7.2, 7.5-10% PEG 6000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 28, 2010 / Details: PT COATED SI MIRRORS |
Radiation | Monochromator: HORIZONTALLY SIDE DIFFRACTING SILICON 111 CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→24.53 Å / Num. obs: 21538 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.8 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: IN-HOUSE STRUCTURE OF DAPK1 Resolution: 2.2→24.53 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.904 / SU B: 11.548 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOOPS AROUND ILE177 AND SER110 SHOW POOR ELECTRON DENSITY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.688 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→24.53 Å
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