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Yorodumi- PDB-5vja: Crystal Structure of human zipper-interacting protein kinase (ZIP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vja | ||||||
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Title | Crystal Structure of human zipper-interacting protein kinase (ZIPK, alias DAPK3) in complex with a pyrazolo[3,4-d]pyrimidinone ligand (HS38) | ||||||
Components | Death-associated protein kinase 3 | ||||||
Keywords | transferase/transferase inhibitor / death-associated protein kinase 3 / transferase / inhibitor / smooth muscle contraction / transferase-transferase inhibitor complex | ||||||
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: 2.46 Å | ||||||
Authors | Carlson, D.A. / Singer, M.R. / Sutherland, C. / Redondo, C. / Alexander, L. / Hughes, P.F. / Knapp, S. / MacDonald, J.A. / Haystead, T.A.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell Chem Biol / Year: 2018 Title: Targeting Pim Kinases and DAPK3 to Control Hypertension. Authors: Carlson, D.A. / Singer, M.R. / Sutherland, C. / Redondo, C. / Alexander, L.T. / Hughes, P.F. / Knapp, S. / Gurley, S.B. / Sparks, M.A. / MacDonald, J.A. / Haystead, T.A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vja.cif.gz | 448.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vja.ent.gz | 368.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vja_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5vja_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5vja_validation.xml.gz | 44.4 KB | Display | |
Data in CIF | 5vja_validation.cif.gz | 61.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/5vja ftp://data.pdbj.org/pub/pdb/validation_reports/vj/5vja | HTTPS FTP |
-Related structure data
Related structure data | 1p4fS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 32545.123 Da / Num. of mol.: 4 / Fragment: UNP residues 9-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK3, ZIPK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O43293, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-DMS / #3: Chemical | ChemComp-DUK / ( #4: Chemical | ChemComp-ILE / | #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: 2.33 Å3/Da / Density % sol: 47.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.9 M Na2-Malonate, pH 6.8 / PH range: 6.8 - 7.5 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2014 |
Radiation | Monochromator: Si [111] CCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→115.02 Å / Num. obs: 42067 / % possible obs: 97 % / Redundancy: 3.2 % / Net I/σ(I): 6.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P4F Resolution: 2.46→115.02 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 18.85 / SU ML: 0.222 / Cross valid method: FREE R-VALUE / ESU R: 0.789 / ESU R Free: 0.287 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.798 Å2
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Refinement step | Cycle: 1 / Resolution: 2.46→115.02 Å
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Refine LS restraints |
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