+Open data
-Basic information
Entry | Database: PDB / ID: 4btm | ||||||
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Title | TTBK1 in complex with inhibitor | ||||||
Components | TAU-TUBULIN KINASE 1 | ||||||
Keywords | TRANSFERASE / LIGAND COMPLEX / STRUCTURE-KINETICS RELATIONSHIP | ||||||
Function / homology | Function and homology information positive regulation of astrocyte activation / positive regulation of cyclin-dependent protein kinase activity / positive regulation of microglial cell activation / positive regulation of cysteine-type endopeptidase activity / microtubule associated complex / positive regulation of protein polymerization / tau-protein kinase activity / substantia nigra development / negative regulation of protein binding / peptidyl-threonine phosphorylation ...positive regulation of astrocyte activation / positive regulation of cyclin-dependent protein kinase activity / positive regulation of microglial cell activation / positive regulation of cysteine-type endopeptidase activity / microtubule associated complex / positive regulation of protein polymerization / tau-protein kinase activity / substantia nigra development / negative regulation of protein binding / peptidyl-threonine phosphorylation / tau protein binding / peptidyl-tyrosine phosphorylation / peptidyl-serine phosphorylation / protein tyrosine kinase activity / learning or memory / non-specific serine/threonine protein kinase / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / positive regulation of gene expression / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | ||||||
Authors | Xue, Y. / Wan, P. / Hillertz, P. / Schweikart, F. / Zhao, Y. / Wissler, L. / Dekker, N. | ||||||
Citation | Journal: Chemmedchem / Year: 2013 Title: X-Ray Structural Analysis of Tau-Tubulin Kinase 1 and its Interactions with Small Molecular Inhibitors. Authors: Xue, Y. / Wan, P.T. / Hillertz, P. / Schweikart, F. / Zhao, Y. / Wissler, L. / Dekker, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4btm.cif.gz | 142.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4btm.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 4btm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/4btm ftp://data.pdbj.org/pub/pdb/validation_reports/bt/4btm | HTTPS FTP |
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-Related structure data
Related structure data | 4btjC 4btkC 1ckiS 1lhxS 2cmwS 2izuS 2v62S 3ggfS 3op5S 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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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38746.543 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 1-313 Source method: isolated from a genetically manipulated source Details: KINASE DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q5TCY1, non-specific serine/threonine protein kinase, tau-protein kinase |
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-Non-polymers , 5 types, 367 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.93 Å3/Da / Density % sol: 78.8 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→43.29 Å / Num. obs: 48993 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 68.15 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.54→2.61 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.8 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CKI, 1LHX, 2CMW, 2IZU, 2V62, 3GGF, 3OP5 Resolution: 2.54→43.29 Å / Cor.coef. Fo:Fc: 0.9467 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.195 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.173 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 56.93 Å2
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Refine analyze | Luzzati coordinate error obs: 0.286 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.54→43.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.54→2.61 Å / Total num. of bins used: 20
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