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Yorodumi- PDB-1yxv: Crystal Structure of Kinase Pim1 in complex with 3,4-Dihydroxy-1-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yxv | ||||||
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Title | Crystal Structure of Kinase Pim1 in complex with 3,4-Dihydroxy-1-methylquinolin-2(1H)-one | ||||||
Components | Proto-oncogene serine/threonine-protein kinase Pim-1 | ||||||
Keywords | TRANSFERASE / Ser/Thr protein kinase | ||||||
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 / ribosomal small subunit binding / transcription factor 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 / ribosomal small subunit binding / transcription factor 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 / positive regulation of brown fat cell differentiation / protein serine/threonine kinase activator activity / negative regulation of innate immune response / 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 Å | ||||||
Authors | Kumar, A. / Mandiyan, V. / Suzuki, Y. / Zhang, C. / Rice, J. / Tsai, J. / Artis, D.R. / Ibrahim, P. / Bremer, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal Structures of Proto-oncogene Kinase Pim1: A Target of Aberrant Somatic Hypermutations in Diffuse Large Cell Lymphoma. Authors: Kumar, A. / Mandiyan, V. / Suzuki, Y. / Zhang, C. / Rice, J. / Tsai, J. / Artis, D.R. / Ibrahim, P. / Bremer, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yxv.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yxv.ent.gz | 54.3 KB | Display | PDB format |
PDBx/mmJSON format | 1yxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/1yxv ftp://data.pdbj.org/pub/pdb/validation_reports/yx/1yxv | 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
#1: Protein | Mass: 33832.320 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P11309, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-IMD / |
#3: Chemical | ChemComp-LI6 / |
#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: 3.8 Å3/Da / Density % sol: 67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Na Acetate, Imidazole, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→84.57 Å / Num. all: 29618 / Num. obs: 29538 / % possible obs: 99.7 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 4 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2→2.05 Å / % possible obs: 99.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 0.8 / Num. measured obs: 2171 / Rsym value: 0.758 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→84.51 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.691 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.5 / ESU R: 0.14 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.693 Å2
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Refinement step | Cycle: LAST / Resolution: 2→84.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 66.774 Å / Origin y: 27.501 Å / Origin z: -0.831 Å
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Refinement TLS group | Selection: ALL |