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- PDB-3obg: Conformational plasticity of p38 MAP kinase DFG mutants in respon... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3obg | ||||||
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Title | Conformational plasticity of p38 MAP kinase DFG mutants in response to inhibitor binding | ||||||
![]() | Mitogen-activated protein kinase 14![]() | ||||||
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Function / homology | ![]() positive regulation of cyclase activity / stress-activated protein kinase signaling cascade / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Namboodiri, H.V. / Karpusas, M. / Bukhtiyarova, M. / Springman, E.B. | ||||||
![]() | ![]() Title: Conformational plasticity of p38 MAP kinase DFG motif mutants in response to inhibitor binding Authors: Namboodiri, H.V. / Springman, E.B. / Karpusas, M. / Bukhtiyarova, M. / Ramcharan, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.7 KB | Display | ![]() |
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PDB format | ![]() | 60.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3mpaC ![]() 3o8pC ![]() 3o8tC ![]() 3o8uC ![]() 3objC ![]() 3oc1C ![]() 1zyjS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 41253.074 Da / Num. of mol.: 1 / Fragment: kinase domain / Mutation: F169G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q16539, ![]() |
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#2: Chemical | ChemComp-SB2 / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.13 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 10-15% PEG 4000, 0.1M Cacodylic acid, 50 mM n-octyl-beta-D-glucoside, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→30.25 Å / Num. obs: 9563 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.143 / Rsym value: 0.109 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.8→3.02 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 1847 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1ZYJ Resolution: 2.8→30.25 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.82 / SU B: 18.853 / SU ML: 0.379 / Cross valid method: THROUGHOUT / ESU R Free: 0.521 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 37.858 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→30.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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