+Open data
-Basic information
Entry | Database: PDB / ID: 2hw7 | ||||||
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Title | Crystal Structure of Mnk2-D228G in complex with Staurosporine | ||||||
Components | MAP kinase-interacting serine/threonine-protein kinase 2 | ||||||
Keywords | TRANSFERASE / protein kinases / drug / inhibitor / phosphorylation | ||||||
Function / homology | Function and homology information calcium-dependent protein serine/threonine kinase activity / cellular response to arsenic-containing substance / calmodulin-dependent protein kinase activity / hemopoiesis / extrinsic apoptotic signaling pathway in absence of ligand / PML body / regulation of translation / cell surface receptor signaling pathway / nuclear body / calmodulin binding ...calcium-dependent protein serine/threonine kinase activity / cellular response to arsenic-containing substance / calmodulin-dependent protein kinase activity / hemopoiesis / extrinsic apoptotic signaling pathway in absence of ligand / PML body / regulation of translation / cell surface receptor signaling pathway / nuclear body / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Jauch, R. / Wahl, M.C. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Mitogen-activated protein kinases interacting kinases are autoinhibited by a reprogrammed activation segment. Authors: Jauch, R. / Cho, M.K. / Netter, C. / Schreiter, K. / Aicher, B. / Zweckstetter, M. / Wahl, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hw7.cif.gz | 71.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hw7.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 2hw7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/2hw7 ftp://data.pdbj.org/pub/pdb/validation_reports/hw/2hw7 | HTTPS FTP |
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-Related structure data
Related structure data | 2hw6C 2ac3S 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: 35604.461 Da / Num. of mol.: 1 / Fragment: Mnk2 / Mutation: D228G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MKNK2, MNK2 / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q9HBH9, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-STU / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.6 Details: Polyacrylic acid, pH 7.6, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98008 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98008 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 12900 / Num. obs: 12862 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Redundancy: 5.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AC3 Resolution: 2.71→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 22.962 / SU ML: 0.227 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.453 / ESU R Free: 0.289 / 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: 69.244 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.71→2.78 Å / 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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