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Yorodumi- PDB-7dhn: The co-crystal structure of DYRK2 with a small molecule inhibitor 20 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dhn | ||||||
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Title | The co-crystal structure of DYRK2 with a small molecule inhibitor 20 | ||||||
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 / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of glycogen biosynthetic process / 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 / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of glycogen biosynthetic process / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Wei, T. / Xiao, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Elife / Year: 2022 Title: Selective inhibition reveals the regulatory function of DYRK2 in protein synthesis and calcium entry. Authors: Wei, T. / Wang, J. / Liang, R. / Chen, W. / Chen, Y. / Ma, M. / He, A. / Du, Y. / Zhou, W. / Zhang, Z. / Zeng, X. / Wang, C. / Lu, J. / Guo, X. / Chen, X.W. / Wang, Y. / Tian, R. / Xiao, J. / Lei, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dhn.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dhn.ent.gz | 116.3 KB | Display | PDB format |
PDBx/mmJSON format | 7dhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/7dhn ftp://data.pdbj.org/pub/pdb/validation_reports/dh/7dhn | HTTPS FTP |
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-Related structure data
Related structure data | 7dg4C 7dh9C 7dhcC 7dhhC 7dhkC 7dhoC 7dhvC 7djoC 7dl6C 3k2lS 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: 37675.633 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-H7R / |
#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: 3.63 Å3/Da / Density % sol: 66.14 % |
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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, 0.01M 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: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→66.32 Å / Num. obs: 298430 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.025 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.38→2.44 Å / Rmerge(I) obs: 1.133 / Num. unique obs: 22578 / CC1/2: 0.789 / Rpim(I) all: 0.334 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K2L Resolution: 2.38→57.836 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.63 / 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: 156.72 Å2 / Biso mean: 66.7205 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.38→57.836 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 77.1066 Å / Origin y: 145.018 Å / Origin z: 3.7793 Å
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Refinement TLS group |
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