+Open data
-Basic information
Entry | Database: PDB / ID: 5a4t | ||||||
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Title | DYRK1A IN COMPLEX WITH NITRILE BENZOTHIAZOLE FRAGMENT | ||||||
Components | DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / amyloid-beta formation ...histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / amyloid-beta formation / negative regulation of DNA damage response, signal transduction by p53 class mediator / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / tubulin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of RNA splicing / peptidyl-threonine phosphorylation / non-membrane spanning protein tyrosine kinase activity / tau protein binding / peptidyl-tyrosine phosphorylation / circadian rhythm / nervous system development / actin binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / protein autophosphorylation / transcription coactivator activity / cytoskeleton / protein kinase activity / nuclear speck / ribonucleoprotein complex / protein phosphorylation / axon / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Rothweiler, U. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Probing the ATP-Binding Pocket of Protein Kinase Dyrk1A with Benzothiazole Fragment Molecules Authors: Rothweiler, U. / Stensen, W. / Brandsdal, B.O. / Isaksson, J. / Leeson, F.A. / Eugh, R.A. / Mjoen Svendsen, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a4t.cif.gz | 280.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a4t.ent.gz | 227.6 KB | Display | PDB format |
PDBx/mmJSON format | 5a4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a4t_validation.pdf.gz | 482.8 KB | Display | wwPDB validaton report |
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Full document | 5a4t_full_validation.pdf.gz | 494 KB | Display | |
Data in XML | 5a4t_validation.xml.gz | 48.8 KB | Display | |
Data in CIF | 5a4t_validation.cif.gz | 65.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/5a4t ftp://data.pdbj.org/pub/pdb/validation_reports/a4/5a4t | HTTPS FTP |
-Related structure data
Related structure data | 5a3xC 5a4eC 5a4lC 5a4qC 5a54C 4nctS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 42653.992 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 126-490 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q13627, dual-specificity kinase #2: Chemical | ChemComp-AJG / #3: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1 M KSCN; 0.1M NACL; 16% 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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2014 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.05→50 Å / Num. obs: 110557 / % possible obs: 98.8 % / Observed criterion σ(I): 1.84 / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12 | |||||||||||||||
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 4 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.84 / % possible all: 95.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4NCT Resolution: 2.15→48.19 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.177 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.038 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.41 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→48.19 Å
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