+Open data
-Basic information
Entry | Database: PDB / ID: 4x7q | ||||||
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Title | PIM2 kinase in complex with Compound 1s | ||||||
Components | Serine/threonine-protein kinase pim-2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information apoptotic mitochondrial changes / positive regulation of macroautophagy / positive regulation of autophagy / regulation of mitotic cell cycle / macroautophagy / G1/S transition of mitotic cell cycle / response to virus / positive regulation of canonical NF-kappaB signal transduction / protein stabilization / non-specific serine/threonine protein kinase ...apoptotic mitochondrial changes / positive regulation of macroautophagy / positive regulation of autophagy / regulation of mitotic cell cycle / macroautophagy / G1/S transition of mitotic cell cycle / response to virus / positive regulation of canonical NF-kappaB signal transduction / protein stabilization / non-specific serine/threonine protein kinase / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Marcotte, D.J. / Silvian, L.F. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2015 Title: Structure-based design of low-nanomolar PIM kinase inhibitors. Authors: Ishchenko, A. / Zhang, L. / Le Brazidec, J.Y. / Fan, J. / Chong, J.H. / Hingway, A. / Raditsis, A. / Singh, L. / Elenbaas, B. / Hong, V.S. / Marcotte, D. / Silvian, L. / Enyedy, I. / Chao, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x7q.cif.gz | 194.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x7q.ent.gz | 153.5 KB | Display | PDB format |
PDBx/mmJSON format | 4x7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/4x7q ftp://data.pdbj.org/pub/pdb/validation_reports/x7/4x7q | HTTPS FTP |
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-Related structure data
Related structure data | 4xhkC 2iwiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 34316.375 Da / Num. of mol.: 2 / Fragment: PIM2 Kinase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIM2 / Production host: Escherichia coli (E. coli) References: UniProt: Q9P1W9, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Sodium Potassium Phosphate / PH range: 7 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 25, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.326→71.132 Å / Num. obs: 19972 / % possible obs: 99.6 % / Redundancy: 2.1 % / Net I/σ(I): 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IWI Resolution: 2.33→43.61 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / SU B: 18.723 / SU ML: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.43 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 113.51 Å2 / Biso mean: 41.034 Å2 / Biso min: 13.43 Å2
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Refinement step | Cycle: final / Resolution: 2.33→43.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.386 Å / Total num. of bins used: 20
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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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