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Yorodumi- PDB-7dh3: The co-crystal structure of DYRK2 with a small molecule inhibitor 5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dh3 | ||||||
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Title | The co-crystal structure of DYRK2 with a small molecule inhibitor 5 | ||||||
Components | Dual specificity tyrosine-phosphorylation-regulated kinase 2 | ||||||
Keywords | CELL CYCLE / kinase / inhibitor | ||||||
Function / homology | Function and homology information dual-specificity kinase / negative regulation of calcineurin-NFAT signaling cascade / smoothened signaling pathway / positive regulation of glycogen biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ubiquitin ligase complex / protein serine/threonine/tyrosine kinase activity / regulation of signal transduction by p53 class mediator / manganese ion binding / protein tyrosine kinase activity ...dual-specificity kinase / negative regulation of calcineurin-NFAT signaling cascade / smoothened signaling pathway / positive regulation of glycogen biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ubiquitin ligase complex / protein serine/threonine/tyrosine kinase activity / regulation of signal transduction by p53 class mediator / manganese ion binding / protein tyrosine kinase activity / Regulation of TP53 Activity through Phosphorylation / cytoskeleton / ribonucleoprotein complex / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Wei, T. / Xiao, J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: The co-crystal structure of DYRK2 with a small molecule inhibitor 5 Authors: Wei, T. / Xiao, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dh3.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dh3.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 7dh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dh3_validation.pdf.gz | 845.5 KB | Display | wwPDB validaton report |
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Full document | 7dh3_full_validation.pdf.gz | 849.7 KB | Display | |
Data in XML | 7dh3_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 7dh3_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/7dh3 ftp://data.pdbj.org/pub/pdb/validation_reports/dh/7dh3 | HTTPS FTP |
-Related structure data
Related structure data | 3k2lS 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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-Components
#1: Protein | Mass: 37871.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK2 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q92630, dual-specificity kinase |
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#2: Chemical | ChemComp-H7C / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 66.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.36 M-0.5 M sodium citrate tribasic dehydrate, 0.01 M sodium borate, pH 7.5-9.5 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→66.22 Å / Num. obs: 23161 / % possible obs: 96.4 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.028 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.33→2.39 Å / Rmerge(I) obs: 1.102 / Num. unique obs: 1751 / CC1/2: 0.807 / Rpim(I) all: 0.311 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K2L Resolution: 2.33→36.417 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.55 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.62 Å2 / Biso mean: 56.1622 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.33→36.417 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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