+Open data
-Basic information
Entry | Database: PDB / ID: 6p5s | ||||||
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Title | HIPK2 kinase domain bound to CX-4945 | ||||||
Components | Homeodomain-interacting protein kinase 2 | ||||||
Keywords | transferase/transferase inhibitor / Homeodomain Interacting Protein / Kinase / p53 regulator / Mitophagy / Fibrosis / NUCLEAR PROTEIN / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information lens induction in camera-type eye / iris morphogenesis / embryonic retina morphogenesis in camera-type eye / embryonic camera-type eye morphogenesis / retina layer formation / Physiological factors / PML body organization / voluntary musculoskeletal movement / eye development / YAP1- and WWTR1 (TAZ)-stimulated gene expression ...lens induction in camera-type eye / iris morphogenesis / embryonic retina morphogenesis in camera-type eye / embryonic camera-type eye morphogenesis / retina layer formation / Physiological factors / PML body organization / voluntary musculoskeletal movement / eye development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / SMAD protein signal transduction / adult walking behavior / virion binding / anterior/posterior pattern specification / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / smoothened signaling pathway / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / Regulation of MECP2 expression and activity / negative regulation of BMP signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of DNA binding / negative regulation of ubiquitin-dependent protein catabolic process / intrinsic apoptotic signaling pathway / erythrocyte differentiation / transforming growth factor beta receptor signaling pathway / SUMOylation of transcription cofactors / regulation of signal transduction by p53 class mediator / positive regulation of JNK cascade / peptidyl-threonine phosphorylation / neuron differentiation / PML body / positive regulation of DNA-binding transcription factor activity / cytoplasmic stress granule / RNA polymerase II transcription regulator complex / positive regulation of angiogenesis / transcription corepressor activity / positive regulation of protein binding / cellular response to hypoxia / peptidyl-serine phosphorylation / protein tyrosine kinase activity / neuron apoptotic process / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / cell population proliferation / transcription coactivator activity / nuclear body / non-specific serine/threonine protein kinase / regulation of cell cycle / protein kinase activity / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 Å | ||||||
Authors | Agnew, C. / Liu, L. / Jura, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: The crystal structure of the protein kinase HIPK2 reveals a unique architecture of its CMGC-insert region. Authors: Agnew, C. / Liu, L. / Liu, S. / Xu, W. / You, L. / Yeung, W. / Kannan, N. / Jablons, D. / Jura, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p5s.cif.gz | 147.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p5s.ent.gz | 119.5 KB | Display | PDB format |
PDBx/mmJSON format | 6p5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/6p5s ftp://data.pdbj.org/pub/pdb/validation_reports/p5/6p5s | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44977.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HIPK2 / Production host: Escherichia coli (E. coli) References: UniProt: Q9H2X6, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-3NG / |
#3: 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: 2.84 Å3/Da / Density % sol: 56.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M KSCN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1111 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1111 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→56.4 Å / Num. obs: 26108 / % possible obs: 99.98 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.021 / Rpim(I) all: 0.021 / Rrim(I) all: 0.03 / Net I/σ(I): 17.63 |
Reflection shell | Resolution: 2.19→2.27 Å / Redundancy: 2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.65 / Num. unique obs: 2564 / CC1/2: 0.857 / Rpim(I) all: 0.24 / Rrim(I) all: 0.35 / % possible all: 99.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.194→56.359 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.194→56.359 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -31.3253 Å / Origin y: 30.2717 Å / Origin z: -0.062 Å
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Refinement TLS group | Selection details: all |