+Open data
-Basic information
Entry | Database: PDB / ID: 6eiq | ||||||
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Title | DYRK1A in complex with XMD14-124 | ||||||
Components | Dual specificity tyrosine-phosphorylation-regulated kinase 1A | ||||||
Keywords | TRANSFERASE / Dual specificity tyrosine-phosphorylation-regulated kinase 1A | ||||||
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 / G0 and Early G1 / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / RNA polymerase II CTD heptapeptide repeat kinase activity ...histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / G0 and Early G1 / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / RNA polymerase II CTD heptapeptide repeat kinase activity / peptidyl-tyrosine autophosphorylation / negative regulation of mRNA splicing, via spliceosome / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / tubulin binding / positive regulation of RNA splicing / peptidyl-threonine phosphorylation / non-membrane spanning protein tyrosine kinase activity / circadian rhythm / tau protein binding / peptidyl-tyrosine phosphorylation / nervous system development / peptidyl-serine phosphorylation / actin binding / protein tyrosine kinase activity / transcription coactivator activity / protein autophosphorylation / 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: 2.3 Å | ||||||
Authors | Rothweiler, U. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eiq.cif.gz | 545.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eiq.ent.gz | 450.9 KB | Display | PDB format |
PDBx/mmJSON format | 6eiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eiq_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6eiq_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6eiq_validation.xml.gz | 50.3 KB | Display | |
Data in CIF | 6eiq_validation.cif.gz | 68.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/6eiq ftp://data.pdbj.org/pub/pdb/validation_reports/ei/6eiq | HTTPS FTP |
-Related structure data
Related structure data | 6eifC 6eijC 6eilC 6eipC 6eirC 6eisC 6eivC 6ej4C 4nctS S: Starting model for refinement C: citing same article (ref.) |
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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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK1A, DYRK, MNB, MNBH / Production host: Escherichia coli (E. coli) / References: UniProt: Q13627, dual-specificity kinase #2: Chemical | ChemComp-B6Z / [ #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: 2.57 Å3/Da / Density % sol: 52.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M KSCN; 0.1M NaCl; 12% PEG 3350, pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984003 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 19, 2016 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.984003 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.3→50 Å / Num. obs: 77090 / % possible obs: 97.1 % / Redundancy: 3.8 % / Net I/σ(I): 9.45 | |||||||||||||||
Reflection shell | Resolution: 2.3→2.44 Å / Mean I/σ(I) obs: 0.99 / Num. unique all: 12348 / Num. unique obs: 48049 / CC1/2: 0.419 / Rrim(I) all: 1.206 / % possible all: 97.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4nct Resolution: 2.3→48.1 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.829 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.05 / 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: 55.491 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→48.1 Å
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Refine LS restraints |
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