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Yorodumi- PDB-4jx7: Crystal structure of Pim1 kinase in complex with inhibitor 2-[(tr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jx7 | ||||||
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Title | Crystal structure of Pim1 kinase in complex with inhibitor 2-[(trans-4-aminocyclohexyl)amino]-4-{[3-(trifluoromethyl)phenyl]amino}pyrido[4,3-d]pyrimidin-5(6H)-one | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Serine/threonine-protein kinases / ATP binding / Phosphorylation / 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 / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / Signaling by FLT3 fusion proteins / positive regulation of brown fat cell differentiation / positive regulation of TORC1 signaling / negative regulation of innate immune response / 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) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Lee, S.J. / Han, B.G. / Cho, J.W. / Choi, J.S. / Lee, J.K. / Song, H.J. / Koh, J.S. / Lee, B.I. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Crystal structure of pim1 kinase in complex with a pyrido[4,3-d]pyrimidine derivative suggests a unique binding mode. Authors: Lee, S.J. / Han, B.G. / Cho, J.W. / Choi, J.S. / Lee, J. / Song, H.J. / Koh, J.S. / Lee, B.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jx7.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jx7.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 4jx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jx7_validation.pdf.gz | 794.8 KB | Display | wwPDB validaton report |
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Full document | 4jx7_full_validation.pdf.gz | 797.1 KB | Display | |
Data in XML | 4jx7_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 4jx7_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/4jx7 ftp://data.pdbj.org/pub/pdb/validation_reports/jx/4jx7 | HTTPS FTP |
-Related structure data
Related structure data | 4jx3C 1xqzS 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: 37293.410 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS References: UniProt: P11309, non-specific serine/threonine protein kinase |
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#2: Protein/peptide | Mass: 1592.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
#3: Chemical | ChemComp-1N6 / |
#4: Water | ChemComp-HOH / |
Sequence details | PIM-1 IS ISOFORM 2 (UNP P11309-2, RESIDUES 92-404). |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.16 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.7 M sodium potassium tartrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2399 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 13, 2010 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2399 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 16996 / % possible obs: 98.3 % |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XQZ Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.118 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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: 38.229 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.463 Å / Total num. of bins used: 20
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