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Open data
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Basic information
Entry | Database: PDB / ID: 3fsk | ||||||
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Title | P38 kinase crystal structure in complex with RO6257 | ||||||
![]() | Mitogen-activated protein kinase 14![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Kuglstatter, A. / Bertrand, J. / Takahara, P. / Villasenor, A. | ||||||
![]() | ![]() Title: Mapping Binding Pocket Volume: Potential Applications towards Ligand Design and Selectivity Authors: Arora, N. / Williams, C. / Delano, W. / Will, D. / Kuglstatter, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.1 KB | Display | ![]() |
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PDB format | ![]() | 63.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3fi4C ![]() 3fklC ![]() 3fknC ![]() 3fkoC ![]() 3fl4C ![]() 1p38 S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The asymmetric unit of the crystal structure contains one biological unit. |
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Components
#1: Protein | ![]() Mass: 42748.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q16539, ![]() |
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#2: Chemical | ChemComp-RO6 / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.67 % |
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Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 50 mM Hepes pH 7.6, 50 mM CaCl2, 17% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→22.51 Å / Num. obs: 31865 / % possible obs: 95.5 % / Redundancy: 4.62 % / Biso Wilson estimate: 12 Å2 / Rsym value: 0.079 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.33 % / Mean I/σ(I) obs: 10.23 / Num. unique all: 2910 / Rsym value: 0.228 / % possible all: 88.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1P38 ![]() 1p38 Resolution: 2→22.51 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 658660.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.8135 Å2 / ksol: 0.413172 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→22.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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