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Yorodumi- PDB-5a6n: Crystal structure of human death associated protein kinase 3 (DAP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a6n | ||||||
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Title | Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with compound 2 | ||||||
Components | DEATH-ASSOCIATED PROTEIN KINASE 3 | ||||||
Keywords | TRANSFERASE / DAPK3 / HUMAN DEATH ASSOCIATED PROTEIN KINASE 3 / DAP-LIKE KINASE / DLK / ZIPPER-INTERACTING PROTEIN KINASE / ZIP-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 / Resolution: 1.7 Å | ||||||
Authors | Rodrigues, T. / Reker, D. / Welin, M. / Caldera, M. / Brunner, C. / Gabernet, G. / Schneider, P. / Walse, B. / Schneider, G. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: De Novo Fragment Design for Drug Discovery and Chemical Biology. Authors: Rodrigues, T. / Reker, D. / Welin, M. / Caldera, M. / Brunner, C. / Gabernet, G. / Schneider, P. / Walse, B. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a6n.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a6n.ent.gz | 99.6 KB | Display | PDB format |
PDBx/mmJSON format | 5a6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a6n_validation.pdf.gz | 472.7 KB | Display | wwPDB validaton report |
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Full document | 5a6n_full_validation.pdf.gz | 477.7 KB | Display | |
Data in XML | 5a6n_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 5a6n_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/5a6n ftp://data.pdbj.org/pub/pdb/validation_reports/a6/5a6n | HTTPS FTP |
-Related structure data
Related structure data | 5a6oC 3bhyS C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.998, 0.049, -0.043), Vector: |
-Components
#1: Protein | Mass: 32545.123 Da / Num. of mol.: 2 / Fragment: PROTEIN KINASE DOMAIN, UNP RESIDUES 9-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O43293, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-U7E / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.6 % / Description: NONE |
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Crystal grow | pH: 6.2 Details: 23% PROPANEDIOL, 0.1M NA/K PHOSPHATE PH 6.2, 10% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2015 |
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→29.71 Å / Num. obs: 71490 / % possible obs: 99.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.6 / % possible all: 98.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BHY Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.875 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUE REFINED INDIVIDUALLY. RESIDUES 170-174 IN CHAIN B ARE DISORDERED.
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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: 26.386 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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