+Open data
-Basic information
Entry | Database: PDB / ID: 2izr | ||||||
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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 / ALTERNATIVE SPLICING / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 | 2izr.cif.gz | 165.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2izr.ent.gz | 128.4 KB | Display | PDB format |
PDBx/mmJSON format | 2izr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/2izr ftp://data.pdbj.org/pub/pdb/validation_reports/iz/2izr | HTTPS FTP |
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-Related structure data
Related structure data | 2izsC 2iztC 2izuC 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 482 molecules
#2: Chemical | ChemComp-BRK / {( | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-PGO / | #6: Water | ChemComp-HOH / | |
-Details
Compound details | CASEIN KINASES ARE OPERATIONALLY DEFINED BY THEIR PREFERENTIAL UTILIZATION OF ACIDIC PROTEINS SUCH ...CASEIN KINASES ARE OPERATIONA |
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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: 2.5 Å3/Da / Density % sol: 51 % |
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Crystal grow | pH: 7 Details: 10% PEG10K, 0.20 M MGCL2, 0.1 M TRIS PH=7.0, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978978 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 4, 2006 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978978 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→49.1 Å / Num. obs: 99653 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.3→1.4 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.8 / % possible all: 79.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CHL Resolution: 1.3→49.15 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.262 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.038 / 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: 15.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→49.15 Å
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