+Open data
-Basic information
Entry | Database: PDB / ID: 8c2z | |||||||||
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Title | Crystal structure of DYRK1B in complex with AZ191 | |||||||||
Components | Dual specificity tyrosine-phosphorylation-regulated kinase 1B | |||||||||
Keywords | TRANSFERASE / Kinase / diabetes / kinase inhibitor | |||||||||
Function / homology | Function and homology information myoblast fusion / dual-specificity kinase / adipose tissue development / protein serine/threonine/tyrosine kinase activity / chromosome / protein tyrosine kinase activity / transcription coactivator activity / protein kinase activity / protein phosphorylation / protein serine kinase activity ...myoblast fusion / dual-specificity kinase / adipose tissue development / protein serine/threonine/tyrosine kinase activity / chromosome / protein tyrosine kinase activity / transcription coactivator activity / protein kinase activity / protein phosphorylation / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | |||||||||
Authors | Grygier, P. / Pustelny, K. / Dubin, G. / Czarna, A. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: To Be Published Title: Structural perspective on the design of selective DYRK1B inhibitors Authors: Grygier, P. / Pustelny, K. / Dubin, G. / Czarna, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c2z.cif.gz | 174.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c2z.ent.gz | 119.9 KB | Display | PDB format |
PDBx/mmJSON format | 8c2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c2z_validation.pdf.gz | 705.1 KB | Display | wwPDB validaton report |
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Full document | 8c2z_full_validation.pdf.gz | 705.6 KB | Display | |
Data in XML | 8c2z_validation.xml.gz | 16 KB | Display | |
Data in CIF | 8c2z_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/8c2z ftp://data.pdbj.org/pub/pdb/validation_reports/c2/8c2z | HTTPS FTP |
-Related structure data
Related structure data | 8c3gC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42904.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK1B, MIRK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y463, dual-specificity kinase | ||||||
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#2: Chemical | ChemComp-QS0 / | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.5 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris pH 5.5, 25% PEG3350, 0.2 M magnesium chloride, 0.1 M manganese (II) chloride. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→45.41 Å / Num. obs: 29064 / % possible obs: 97.1 % / Redundancy: 8.3 % / Biso Wilson estimate: 38.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.029 / Rrim(I) all: 0.083 / Χ2: 1.04 / Net I/σ(I): 13.8 / Num. measured all: 242154 |
Reflection shell | Resolution: 1.91→1.95 Å / % possible obs: 97.8 % / Redundancy: 8.5 % / Rmerge(I) obs: 2.035 / Num. measured all: 16608 / Num. unique obs: 1945 / CC1/2: 0.453 / Rpim(I) all: 0.726 / Rrim(I) all: 2.164 / Χ2: 1.08 / Net I/σ(I) obs: 1.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→45.41 Å / SU ML: 0.2807 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7947 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→45.41 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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