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Open data
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Basic information
Entry | Database: PDB / ID: 6eif | ||||||
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Title | DYRK1A in complex with XMD7-117 | ||||||
![]() | Dual specificity tyrosine-phosphorylation-regulated kinase 1A![]() | ||||||
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Function / homology | ![]() histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rothweiler, U. | ||||||
![]() | ![]() Title: Novel Scaffolds for Dual Specificity Tyrosine-Phosphorylation-Regulated Kinase (DYRK1A) Inhibitors. Authors: Czarna, A. / Wang, J. / Zelencova, D. / Liu, Y. / Deng, X. / Choi, H.G. / Zhang, T. / Zhou, W. / Chang, J.W. / Kildalsen, H. / Seternes, O.M. / Gray, N.S. / Engh, R.A. / Rothweiler, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 526.2 KB | Display | ![]() |
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PDB format | ![]() | 435.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6eijC ![]() 6eilC ![]() 6eipC ![]() 6eiqC ![]() 6eirC ![]() 6eisC ![]() 6eivC ![]() 6ej4C ![]() 4nctS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 42653.992 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Phosphotyrosine / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-B5T / #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.62 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M KSCN; 0.1M NaCl; 14% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 11, 2016 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.22→50 Å / Num. obs: 89260 / % possible obs: 99.1 % / Redundancy: 4.9 % / Rrim(I) all: 0.149 / Net I/σ(I): 8.6 | |||||||||||||||
Reflection shell | Resolution: 1.93→2.22 Å / Mean I/σ(I) obs: 1.93 / Num. measured obs: 68970 / Num. unique all: 13806 / CC1/2: 0.743 / Rrim(I) all: 0.775 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4nct Resolution: 2.22→48.57 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.901 / SU B: 9.364 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.044 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.94 Å2
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Refinement step | Cycle: 1 / Resolution: 2.22→48.57 Å
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Refine LS restraints |
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