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Open data
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Basic information
Entry | Database: PDB / ID: 7a55 | ||||||
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Title | Structure of DYRK1A in complex with compound 8 | ||||||
![]() | 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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Dokurno, P. / Surgenor, A.E. / Hubbard, R.E. | ||||||
![]() | ![]() Title: Fragment-Derived Selective Inhibitors of Dual-Specificity Kinases DYRK1A and DYRK1B. Authors: Lee Walmsley, D. / Murray, J.B. / Dokurno, P. / Massey, A.J. / Benwell, K. / Fiumana, A. / Foloppe, N. / Ray, S. / Smith, J. / Surgenor, A.E. / Edmonds, T. / Demarles, D. / Burbridge, M. / ...Authors: Lee Walmsley, D. / Murray, J.B. / Dokurno, P. / Massey, A.J. / Benwell, K. / Fiumana, A. / Foloppe, N. / Ray, S. / Smith, J. / Surgenor, A.E. / Edmonds, T. / Demarles, D. / Burbridge, M. / Cruzalegui, F. / Kotschy, A. / Hubbard, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.5 KB | Display | ![]() |
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PDB format | ![]() | 122.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7a4oC ![]() 7a4rC ![]() 7a4sC ![]() 7a4wC ![]() 7a4zC ![]() 7a51C ![]() 7a52C ![]() 7a53C ![]() 7a5bC ![]() 7a5dC ![]() 7a5lC ![]() 7a5nC ![]() 2vx3S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 44553.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.34 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1M MES buffer at pH 6.5, 12% Peg3350, 0.2M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→50 Å / Num. obs: 38587 / % possible obs: 96.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3611 / % possible all: 91.1 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2vx3 Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.436 / SU ML: 0.19 / SU R Cruickshank DPI: 0.2709 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.17 Å2 / Biso mean: 37.152 Å2 / Biso min: 16.39 Å2
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Refinement step | Cycle: final / Resolution: 2.2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.203→2.321 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
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