+Open data
-Basic information
Entry | Database: PDB / ID: 7q90 | ||||||
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Title | Crystal structure of TTBK2 in complex with VNG1.63 (compound 32) | ||||||
Components | Tau-tubulin kinase 2 | ||||||
Keywords | TRANSFERASE / kinase / TTBK2 / tau tubulin kinase / kinase inhibitor | ||||||
Function / homology | Function and homology information negative regulation of protein localization to microtubule / negative regulation of microtubule binding / cerebellar granular layer development / cerebellar granule cell precursor tangential migration / ciliary transition zone / negative regulation of microtubule depolymerization / microtubule plus-end binding / smoothened signaling pathway / tau-protein kinase activity / kinesin binding ...negative regulation of protein localization to microtubule / negative regulation of microtubule binding / cerebellar granular layer development / cerebellar granule cell precursor tangential migration / ciliary transition zone / negative regulation of microtubule depolymerization / microtubule plus-end binding / smoothened signaling pathway / tau-protein kinase activity / kinesin binding / cilium assembly / Anchoring of the basal body to the plasma membrane / regulation of cell migration / centriole / cerebellum development / ciliary basal body / tau protein binding / microtubule cytoskeleton organization / peptidyl-serine phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / extracellular space / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Chaikuad, A. / Nozal, V. / Martinez, A. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: TDP-43 Modulation by Tau-Tubulin Kinase 1 Inhibitors: A New Avenue for Future Amyotrophic Lateral Sclerosis Therapy. Authors: Nozal, V. / Martinez-Gonzalez, L. / Gomez-Almeria, M. / Gonzalo-Consuegra, C. / Santana, P. / Chaikuad, A. / Perez-Cuevas, E. / Knapp, S. / Lietha, D. / Ramirez, D. / Petralla, S. / Monti, B. ...Authors: Nozal, V. / Martinez-Gonzalez, L. / Gomez-Almeria, M. / Gonzalo-Consuegra, C. / Santana, P. / Chaikuad, A. / Perez-Cuevas, E. / Knapp, S. / Lietha, D. / Ramirez, D. / Petralla, S. / Monti, B. / Gil, C. / Martin-Requero, A. / Palomo, V. / de Lago, E. / Martinez, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q90.cif.gz | 268.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q90.ent.gz | 216.3 KB | Display | PDB format |
PDBx/mmJSON format | 7q90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q90_validation.pdf.gz | 949.8 KB | Display | wwPDB validaton report |
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Full document | 7q90_full_validation.pdf.gz | 955.7 KB | Display | |
Data in XML | 7q90_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 7q90_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/7q90 ftp://data.pdbj.org/pub/pdb/validation_reports/q9/7q90 | HTTPS FTP |
-Related structure data
Related structure data | 7q8vC 7q8wC 7q8yC 7q8zC 7qhwC 6u0kS 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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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 7 - 298 / Label seq-ID: 8 - 299
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-Components
#1: Protein | Mass: 34467.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTBK2, KIAA0847 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 References: UniProt: Q6IQ55, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | 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: 2.81 Å3/Da / Density % sol: 56.23 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.6M Na/K phosphate pH 7, 5% Glycerol, 0.1M tris 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 18, 2021 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.6→46.4 Å / Num. obs: 102884 / % possible obs: 99.8 % / Redundancy: 10.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.033 / Rrim(I) all: 0.106 / Net I/σ(I): 16.9 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6u0k Resolution: 1.6→46.4 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.184 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0854 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.087 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.03 Å2 / Biso mean: 21.648 Å2 / Biso min: 8.63 Å2
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Refinement step | Cycle: final / Resolution: 1.6→46.4 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 9410 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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