+Open data
-Basic information
Entry | Database: PDB / ID: 6qxk | ||||||
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Title | Human PIM1 bound to OX0999 | ||||||
Components |
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Keywords | TRANSFERASE / Kinase / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / 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 / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / 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 / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / 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 / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Alexander, L.T. / Elkins, J.M. / Russell, A. / Bountra, C. / Edwards, A.M. / Knapp, S. | ||||||
Citation | Journal: To Be Published Title: PIM1 bound to OX0999 Authors: Knapp, S. / Elkins, J.M. / Alexander, L.T. / Russell, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qxk.cif.gz | 129.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qxk.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 6qxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qxk_validation.pdf.gz | 737.8 KB | Display | wwPDB validaton report |
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Full document | 6qxk_full_validation.pdf.gz | 737.8 KB | Display | |
Data in XML | 6qxk_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 6qxk_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/6qxk ftp://data.pdbj.org/pub/pdb/validation_reports/qx/6qxk | HTTPS FTP |
-Related structure data
Related structure data | 2c3iS 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: 35590.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pLIC-SGC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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: obtained synthetically / Source: (synth.) unidentified (others) |
#3: Chemical | ChemComp-JKW / |
#4: 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: 2.99 Å3/Da / Density % sol: 58.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M NaNO3, 0.1M bis-tris propane pH 8.5, 20% PEG 3350, 10% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→84.77 Å / Num. obs: 25672 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3737 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2C3I Resolution: 2.1→84.77 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.794 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.469 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→84.77 Å
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