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Yorodumi- PDB-5kgk: Crystal structure of PIM1 with inhibitor: 3-(4-methoxyphenyl)-1~{... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kgk | ||||||
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Title | Crystal structure of PIM1 with inhibitor: 3-(4-methoxyphenyl)-1~{H}-pyrazol-5-amine | ||||||
Components | Serine/threonine-protein kinase pim-1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Kinase / transferase / Serine/threonine-protein kinase pim-1 / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / Signaling by FLT3 fusion proteins ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / Signaling by FLT3 fusion proteins / positive regulation of TORC1 signaling / negative regulation of innate immune response / positive regulation of brown fat cell differentiation / protein serine/threonine kinase activator activity / regulation of transmembrane transporter activity / positive regulation of protein serine/threonine kinase activity / negative regulation of DNA-binding transcription factor activity / cellular response to type II interferon / manganese ion binding / Interleukin-4 and Interleukin-13 signaling / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / negative regulation of apoptotic process / apoptotic process / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å | ||||||
Authors | Ferguson, A.D. | ||||||
Citation | Journal: To Be Published Title: Structure of PIM1 in complex with inhibitor Authors: Ferguson, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kgk.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kgk.ent.gz | 99 KB | Display | PDB format |
PDBx/mmJSON format | 5kgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/5kgk ftp://data.pdbj.org/pub/pdb/validation_reports/kg/5kgk | HTTPS FTP |
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-Related structure data
Related structure data | 5kgdC 5kgeC 5kggC 5kgiC 4dtkS C: citing same article (ref.) S: Starting model for refinement |
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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: 31905.203 Da / Num. of mol.: 1 / Fragment: UNP residues 30-305 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli (E. coli) References: UniProt: P11309, non-specific serine/threonine protein kinase | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-6SD / | #4: Chemical | #5: 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: 3.58 Å3/Da / Density % sol: 65.62 % |
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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: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9173 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 25, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→58.99 Å / Num. obs: 13046 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 81.24 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 35.2 |
Reflection shell | Resolution: 2.66→2.8 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 4.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DTK Resolution: 2.66→58.99 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.387 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.36 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.23
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Displacement parameters | Biso mean: 64.01 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.66→58.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.66→2.87 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: 30.7295 Å / Origin y: 27.6052 Å / Origin z: 0.301 Å
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Refinement TLS group | Selection details: { A|* } |