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Yorodumi- PDB-7dl6: The co-crystal structure of DYRK2 with a small molecule inhibitor 18 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dl6 | ||||||
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Title | The co-crystal structure of DYRK2 with a small molecule inhibitor 18 | ||||||
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: 2.648 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 | 7dl6.cif.gz | 151.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dl6.ent.gz | 117.4 KB | Display | PDB format |
PDBx/mmJSON format | 7dl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dl6_validation.pdf.gz | 824.5 KB | Display | wwPDB validaton report |
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Full document | 7dl6_full_validation.pdf.gz | 829.8 KB | Display | |
Data in XML | 7dl6_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 7dl6_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/7dl6 ftp://data.pdbj.org/pub/pdb/validation_reports/dl/7dl6 | HTTPS FTP |
-Related structure data
Related structure data | 7dg4C 7dh9C 7dhcC 7dhhC 7dhkC 7dhnC 7dhoC 7dhvC 7djoC 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-H96 / [ |
#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: 3.65 Å3/Da / Density % sol: 66.34 % |
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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, pH7.5-9.5 |
-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: Dec 8, 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: 2.648→50 Å / Num. obs: 16370 / % possible obs: 99.2 % / Redundancy: 8.3 % / CC1/2: 0.991 / Rpim(I) all: 0.053 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.65→2.74 Å / Rmerge(I) obs: 0.452 / Num. unique obs: 15541 / CC1/2: 0.816 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K2L Resolution: 2.648→43.545 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.32 / 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: 137.75 Å2 / Biso mean: 46.2211 Å2 / Biso min: 15.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.648→43.545 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 76.9029 Å / Origin y: 145.1761 Å / Origin z: 3.6284 Å
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Refinement TLS group |
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