+Open data
-Basic information
Entry | Database: PDB / ID: 4aze | ||||||
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Title | Human DYRK1A in complex with Leucettine L41 | ||||||
Components | (DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1ADYRK1A) x 2 | ||||||
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 / negative regulation of DNA damage response, signal transduction by p53 class mediator ...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 / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / 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 / tau protein binding / non-membrane spanning protein tyrosine kinase activity / 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: 3.15 Å | ||||||
Authors | Elkins, J.M. / Soundararajan, M. / Muniz, J.R.C. / Tahtouh, T. / Burgy, G. / Durieu, E. / Lozach, O. / Cochet, C. / Schmid, R.S. / Lo, D.C. ...Elkins, J.M. / Soundararajan, M. / Muniz, J.R.C. / Tahtouh, T. / Burgy, G. / Durieu, E. / Lozach, O. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Carreaux, F. / Bazureau, J.P. / Meijer, L. / Edwards, A. / Bountra, C. / Knapp, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Selectivity, Co-Crystal Structures and Neuroprotective Properties of Leucettines, a Family of Protein Kinase Inhibitors Derived from the Marine Sponge Alkaloid Leucettamine B. Authors: Tahtouh, T. / Elkins, J.M. / Filippakopoulos, P. / Soundararajan, M. / Burgy, G. / Durieu, E. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Oberholzer, A. / Laurence, P. / ...Authors: Tahtouh, T. / Elkins, J.M. / Filippakopoulos, P. / Soundararajan, M. / Burgy, G. / Durieu, E. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Oberholzer, A. / Laurence, P. / Carreaux, F. / Bazureau, J.P. / Knapp, S. / Meijer, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aze.cif.gz | 448 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aze.ent.gz | 372.7 KB | Display | PDB format |
PDBx/mmJSON format | 4aze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/4aze ftp://data.pdbj.org/pub/pdb/validation_reports/az/4aze | HTTPS FTP |
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-Related structure data
Related structure data | 4azfC 4b7tC 4gw8C 2vx3S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 44633.164 Da / Num. of mol.: 3 / Fragment: KINASE DOMAIN, RESIDUES 128-485 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q13627, dual-specificity kinase, non-specific serine/threonine protein kinase #2: Protein/peptide | Mass: 440.386 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: UNKNOWN PARTS OF THE N-TERMINUS / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: dual-specificity kinase, non-specific serine/threonine protein kinase #3: Chemical | Sequence details | UNKNOWN PARTS OF THE N-TERMINUS OF CHAINS A,B,C HAVE BEEN MODELLED AS CHAINS E,F,G | |
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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: 4.1 Å3/Da / Density % sol: 69.8 % / Description: NONE |
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Crystal grow | pH: 8.2 Details: 0.03 M MGCL2, 22% POLYACRYLIC ACID 5100, 0.1 M HEPES PH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.984 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 28, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→100.57 Å / Num. obs: 37756 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 3.15→3.32 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VX3 Resolution: 3.15→100.57 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.909 / SU B: 49.158 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R: 1.813 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.693 Å2
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Refinement step | Cycle: LAST / Resolution: 3.15→100.57 Å
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Refine LS restraints |
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