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Yorodumi- PDB-2xix: Protein kinase Pim-1 in complex with fragment-1 from crystallogra... -
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-Basic information
Entry | Database: PDB / ID: 2xix | ||||||
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Title | Protein kinase Pim-1 in complex with fragment-1 from crystallographic fragment screen | ||||||
Components | PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1 | ||||||
Keywords | TRANSFERASE / ATP-BINDING / PHOSPHORYLATION | ||||||
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 / negative regulation of innate immune response ...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 / negative regulation of innate immune response / Signaling by FLT3 fusion proteins / positive regulation of brown fat cell differentiation / positive regulation of TORC1 signaling / 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 / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / nucleolus / 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: 2.4 Å | ||||||
Authors | Schulz, M.N. / Fanghanel, J. / Schafer, M. / Badock, V. / Briem, H. / Boemer, U. / Nguyen, D. / Husemann, M. / Hillig, R.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2011 Title: Crystallographic Fragment Screen Identifies Cinnamic Acid Derivatives as Starting Points for Potent Pim-1 Inhibitors Authors: Schulz, M.N. / Fanghanel, J. / Schafer, M. / Badock, V. / Briem, H. / Boemer, U. / Nguyen, D. / Husemann, M. / Hillig, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xix.cif.gz | 130 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xix.ent.gz | 101.5 KB | Display | PDB format |
PDBx/mmJSON format | 2xix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xix_validation.pdf.gz | 446.9 KB | Display | wwPDB validaton report |
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Full document | 2xix_full_validation.pdf.gz | 448.3 KB | Display | |
Data in XML | 2xix_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 2xix_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/2xix ftp://data.pdbj.org/pub/pdb/validation_reports/xi/2xix | HTTPS FTP |
-Related 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: 34468.910 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 14-313 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET30A, HIS-TEV-PIM-1(14-313) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P11309, EC: 2.7.1.37, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-XIX / |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
Sequence details | N-TERMINAL GLY FROM TEV CLEAVAGE SITE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.8 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 0.9 M (NH4)2HPO4, 0.1 M SODIUM CITRATE PH=5.5, 0.2M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 29, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→42.1 Å / Num. obs: 15473 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.1 / % possible all: 51.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE PIM STRUCTURE Resolution: 2.4→42.11 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.84 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.033 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→42.11 Å
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