+Open data
-Basic information
Entry | Database: PDB / ID: 2izu | ||||||
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Title | Structure of casein kinase gamma 3 in complex with inhibitor | ||||||
Components | CASEIN KINASE I ISOFORM GAMMA-3 | ||||||
Keywords | TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / KINASE / ATP- BINDING / PHOSPHORYLATION / NUCLEOTIDE-BINDING / WNT SIGNALING PATHWAY / SERINE/THREONINE KINASE | ||||||
Function / homology | Function and homology information protein modification process / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction ...protein modification process / Wnt signaling pathway / endocytosis / positive regulation of canonical Wnt signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Bunkoczi, G. / Salah, E. / Rellos, P. / Das, S. / Fedorov, O. / Savitsky, P. / Debreczeni, J.E. / Gileadi, O. / Sundstrom, M. / Edwards, A. ...Bunkoczi, G. / Salah, E. / Rellos, P. / Das, S. / Fedorov, O. / Savitsky, P. / Debreczeni, J.E. / Gileadi, O. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / von Delft, F. / Knapp, S. | ||||||
Citation | Journal: To be Published Title: Inhibitor Binding by Casein Kinases Authors: Bunkoczi, G. / Salah, E. / Rellos, P. / Das, S. / Fedorov, O. / Savitsky, P. / Debreczeni, J.E. / Gileadi, O. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / von Delft, F. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2izu.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2izu.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 2izu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2izu_validation.pdf.gz | 800.9 KB | Display | wwPDB validaton report |
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Full document | 2izu_full_validation.pdf.gz | 801.9 KB | Display | |
Data in XML | 2izu_validation.xml.gz | 17 KB | Display | |
Data in CIF | 2izu_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/2izu ftp://data.pdbj.org/pub/pdb/validation_reports/iz/2izu | HTTPS FTP |
-Related structure data
Related structure data | 2izrC 2izsC 2iztC 2chlS 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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Unit cell |
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-Components
#1: Protein | Mass: 38557.395 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC-SGC / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9Y6M4, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-P01 / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
Compound details | CASEIN KINASES ARE OPERATIONALLY DEFINED BY THEIR PREFERENTIAL UTILIZATION OF ACIDIC PROTEINS SUCH ...CASEIN KINASES ARE OPERATIONA |
-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 | Details: 20% PEG3350, 0.20 M NAFORMATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Apr 23, 2006 |
Radiation | Monochromator: OSMIC HR MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→28.5 Å / Num. obs: 32225 / % possible obs: 80.7 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.6 / % possible all: 24.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CHL Resolution: 1.85→27.57 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.092 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.121 / 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: 12.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→27.57 Å
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