+Open data
-Basic information
Entry | Database: PDB / ID: 5a4e | ||||||
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Title | DYRK1A in complex with methoxy 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 DNA damage response, signal transduction by p53 class mediator / 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 DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / negative regulation of mRNA splicing, via spliceosome / 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 / circadian rhythm / peptidyl-tyrosine phosphorylation / : / 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 / axon / protein phosphorylation / 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: 2.68 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 | 5a4e.cif.gz | 512.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a4e.ent.gz | 427.3 KB | Display | PDB format |
PDBx/mmJSON format | 5a4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a4e_validation.pdf.gz | 489.3 KB | Display | wwPDB validaton report |
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Full document | 5a4e_full_validation.pdf.gz | 500.8 KB | Display | |
Data in XML | 5a4e_validation.xml.gz | 45.1 KB | Display | |
Data in CIF | 5a4e_validation.cif.gz | 59.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/5a4e ftp://data.pdbj.org/pub/pdb/validation_reports/a4/5a4e | HTTPS FTP |
-Related structure data
Related structure data | 5a3xC 5a4lC 5a4qC 5a4tC 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: 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-7QQ / #3: Water | ChemComp-HOH / | |
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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: 2.5 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1 M KSCN; 0.1M KCL; 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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.68→50 Å / Num. obs: 48593 / % possible obs: 98.5 % / Observed criterion σ(I): 1.55 / Redundancy: 5.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.8 | |||||||||||||||
Reflection shell | Resolution: 2.68→2.84 Å / Redundancy: 5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.55 / % possible all: 92.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4NCT Resolution: 2.68→47.54 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.846 / SU B: 18.503 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 57.057 Å2
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Refinement step | Cycle: LAST / Resolution: 2.68→47.54 Å
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