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- PDB-5kge: Crystal structure of PIM1 with inhibitor: 5-(3,4-dichlorophenyl)-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kge | ||||||
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Title | Crystal structure of PIM1 with inhibitor: 5-(3,4-dichlorophenyl)-1~{H}-pyrazol-3-amine | ||||||
![]() | Serine/threonine-protein kinase pim-1 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / ![]() ![]() | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Ferguson, A.D. | ||||||
![]() | ![]() Title: Structure of PIM1 in complex with inhibitor Authors: Ferguson, A.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.9 KB | Display | ![]() |
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PDB format | ![]() | 100.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5kgdC ![]() 5kggC ![]() 5kgiC ![]() 5kgkC ![]() 4dtkS 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: 31905.203 Da / Num. of mol.: 1 / Fragment: UNP residues 30-305 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P11309, ![]() | ||||||
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#2: Chemical | ChemComp-EDO / ![]() #3: Chemical | ChemComp-6SN / | #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.13 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 18% PEG 3350, 0.2 M Na2SO4, 6% ethylene glycol, 0.1 M Tris, pH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.23→58.19 Å / Num. obs: 21136 / % possible obs: 99.7 % / Redundancy: 11.3 % / Biso Wilson estimate: 49.74 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 2.23→2.35 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4DTK Resolution: 2.23→58.19 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.926 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.19 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.155
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Displacement parameters | Biso mean: 53.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.23→58.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.34 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Origin x: 38.8262 Å / Origin y: -12.6165 Å / Origin z: 0.3404 Å
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Refinement TLS group | Selection details: { A|* } |