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Yorodumi- PDB-3bhy: Crystal structure of human death associated protein kinase 3 (DAP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bhy | ||||||
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Title | Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with a beta-carboline ligand | ||||||
Components | Death-associated protein kinase 3 | ||||||
Keywords | TRANSFERASE / Death Associated Kinase / DAPK3 / ZIP kinase / ZIPK / DAP kinase 3 / DAP like kinase / Dlk / Structural Genomics Consortium / SGC / Apoptosis / ATP-binding / Chromatin regulator / Nucleotide-binding / Nucleus / Serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information regulation of myosin II filament organization / leucine zipper domain binding / cAMP response element binding protein binding / regulation of smooth muscle contraction / regulation of cell motility / Caspase activation via Dependence Receptors in the absence of ligand / regulation of focal adhesion assembly / regulation of mitotic nuclear division / regulation of mitotic cell cycle / regulation of autophagy ...regulation of myosin II filament organization / leucine zipper domain binding / cAMP response element binding protein binding / regulation of smooth muscle contraction / regulation of cell motility / Caspase activation via Dependence Receptors in the absence of ligand / regulation of focal adhesion assembly / regulation of mitotic nuclear division / regulation of mitotic cell cycle / regulation of autophagy / regulation of actin cytoskeleton organization / apoptotic signaling pathway / PML body / cellular response to type II interferon / small GTPase binding / positive regulation of canonical Wnt signaling pathway / chromatin organization / regulation of cell shape / regulation of apoptotic process / protein autophosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / intracellular signal transduction / positive regulation of cell migration / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / apoptotic process / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.24 Å | ||||||
Authors | Filippakopoulos, P. / Rellos, P. / Eswaran, J. / Fedorov, O. / Berridge, G. / Niesen, F. / Bracher, F. / Huber, K. / Pike, A.C.W. / Roos, A. ...Filippakopoulos, P. / Rellos, P. / Eswaran, J. / Fedorov, O. / Berridge, G. / Niesen, F. / Bracher, F. / Huber, K. / Pike, A.C.W. / Roos, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: 7,8-dichloro-1-oxo-beta-carbolines as a versatile scaffold for the development of potent and selective kinase inhibitors with unusual binding modes. Authors: Huber, K. / Brault, L. / Fedorov, O. / Gasser, C. / Filippakopoulos, P. / Bullock, A.N. / Fabbro, D. / Trappe, J. / Schwaller, J. / Knapp, S. / Bracher, F. | ||||||
History |
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Remark 600 | HETEROGEN AUTHORS STATE THAT ACCORDING TO ELECTRON DENSITY MAPS, ONE OF TWO CHLORINE ATOMS OF THE ... HETEROGEN AUTHORS STATE THAT ACCORDING TO ELECTRON DENSITY MAPS, ONE OF TWO CHLORINE ATOMS OF THE LIGAND 7CP (NAMELY CL1F) SEEMS TO BE CLEAVED. AUTHORS REFINED ITS OCCUPANCY AS 50% AND STILL WERE ABLE TO IDENTIFY AN EXTRA DENSITY PRESENT BETWEEN THE TWO CHLORINES (NAMELY CL1F AND CL1E). THIS EXTRA DENSITY HAS BEEN MODELED AS A CHLORIDE ION (NAMELY CL). AUTHORS CAN NOT EXPLAIN WHY THE CARBON-CHLORINE BOND WAS BROKEN, HOWEVER THEY DO SUSPECT THAT THE PHOTOLYTIC CLEAVAGE IS THE ANSWER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bhy.cif.gz | 137.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bhy.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 3bhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bhy_validation.pdf.gz | 746 KB | Display | wwPDB validaton report |
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Full document | 3bhy_full_validation.pdf.gz | 746.9 KB | Display | |
Data in XML | 3bhy_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 3bhy_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/3bhy ftp://data.pdbj.org/pub/pdb/validation_reports/bh/3bhy | HTTPS FTP |
-Related structure data
Related structure data | 3cxwC 3cy2C 1yrpS 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: 32545.123 Da / Num. of mol.: 1 / Fragment: Protein kinase domain: Residues 9-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK3, ZIPK / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(R3) References: UniProt: O43293, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-7CP / ( |
#4: 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: 1.91 Å3/Da / Density % sol: 35.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1M SPG (sucrose-phosphate-glutamate buffer) pH 6.0, 30% PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97926 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 19, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.7 % / Av σ(I) over netI: 8.6 / Number: 254440 / Rmerge(I) obs: 0.079 / Χ2: 1.05 / D res high: 1.24 Å / D res low: 50 Å / Num. obs: 68373 / % possible obs: 99.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.24→50 Å / Num. all: 68642 / Num. obs: 68318 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 14.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.24→1.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 2.04 / Num. unique all: 6829 / Rsym value: 0.707 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1YRP Resolution: 1.24→45.36 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.561 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 15.982 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→45.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.24→1.27 Å / Total num. of bins used: 20
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