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- PDB-5n50: Crystal structure of human Pim-1 kinase in complex with a consens... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5n50 | ||||||
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Title | Crystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment like molecule 2-(4-chlorophenyl)sulfanylacetohydrazide | ||||||
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Function / homology | ![]() positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Siefker, C. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: A crystallographic fragment study with human Pim-1 kinase Authors: Siefker, C. / Heine, A. / Hardes, K. / Steinmetzer, A. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133 KB | Display | ![]() |
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PDB format | ![]() | 102.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5mzlC ![]() 5n4nC ![]() 5n4oC ![]() 5n4rC ![]() 5n4uC ![]() 5n4vC ![]() 5n4xC ![]() 5n4yC ![]() 5n4zC ![]() 5n51C ![]() 5n52C ![]() 5n5lC ![]() 5n5mC ![]() 5ndtC ![]() 3we8S 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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Unit cell |
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Components
#1: Protein | Mass: 35632.602 Da / Num. of mol.: 1 / Mutation: R250G Source method: isolated from a genetically manipulated source Details: Isofrom 2 of PIM-1 kinase / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P11309, ![]() |
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#2: Protein/peptide | Mass: 1592.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PIM-1 consensus peptide / Source: (synth.) ![]() ![]() |
#3: Chemical | ChemComp-8MN / |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 61 % / Description: hexagonal rod |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: HEPES CaCl2 Glycerol DTT BIS-TRIS-propane PEG3350 Ethylene-glycol DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 27, 2016 / Details: Silicon |
Radiation | Monochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.92→50 Å / Num. obs: 33834 / % possible obs: 99.9 % / Redundancy: 7.99 % / CC1/2: 0.99 / Rrim(I) all: 0.086 / Net I/σ(I): 15.01 |
Reflection shell | Resolution: 1.92→2.04 Å / Redundancy: 8.07 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 5425 / CC1/2: 0.91 / Rrim(I) all: 0.544 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3WE8 Resolution: 1.92→41.954 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→41.954 Å
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Refine LS restraints |
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LS refinement shell |
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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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