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Yorodumi- PDB-2xiy: Protein kinase Pim-1 in complex with fragment-2 from crystallogra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xiy | ||||||
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Title | Protein kinase Pim-1 in complex with fragment-2 from crystallographic fragment screen | ||||||
Components | PROTO-ONCOGENE SERINE/THREONINE PROTEIN KINASE PIM-1 | ||||||
Keywords | TRANSFERASE / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / 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 / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / 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 / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 2xiy.cif.gz | 132.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xiy.ent.gz | 103 KB | Display | PDB format |
PDBx/mmJSON format | 2xiy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/2xiy ftp://data.pdbj.org/pub/pdb/validation_reports/xi/2xiy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34388.934 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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-Non-polymers , 5 types, 136 molecules
#2: Chemical | ChemComp-XIY / |
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#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | GLYCEROL (GOL): ARTIFACT FROM CRYO BUFFER CHLORIDE ION (CL): ARTIFACT FROM CRYSTALLIZATION BUFFER ...GLYCEROL (GOL): ARTIFACT FROM CRYO BUFFER CHLORIDE ION (CL): ARTIFACT FROM CRYSTALLIZ |
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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: SOLVED BY RIGID BODY REFINEMENT |
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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: 2.2→48.6 Å / Num. obs: 21175 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.25 / % possible all: 71.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE PIM-1 STRUCTURE Resolution: 2.2→48.62 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.666 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.159 / 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: 18.238 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→48.62 Å
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