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Yorodumi- PDB-4lmu: Crystal structure of Pim1 in complex with the inhibitor Quercetin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lmu | ||||||
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Title | Crystal structure of Pim1 in complex with the inhibitor Quercetin (resulting from displacement of SKF86002) | ||||||
Components | Serine/threonine-protein kinase pim-1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / co-crystallization / SKF86002 / fluorescence / inhibitor screening / kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 / negative regulation of innate immune response / 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 / molecular replacement / Resolution: 2.38 Å | ||||||
Authors | Parker, L.J. / Tanaka, A. / Handa, N. / Honda, K. / Tomabechi, Y. / Shirouzu, M. / Yokoyama, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Kinase crystal identification and ATP-competitive inhibitor screening using the fluorescent ligand SKF86002. Authors: Parker, L.J. / Taruya, S. / Tsuganezawa, K. / Ogawa, N. / Mikuni, J. / Honda, K. / Tomabechi, Y. / Handa, N. / Shirouzu, M. / Yokoyama, S. / Tanaka, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lmu.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lmu.ent.gz | 97.3 KB | Display | PDB format |
PDBx/mmJSON format | 4lmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/4lmu ftp://data.pdbj.org/pub/pdb/validation_reports/lm/4lmu | HTTPS FTP |
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-Related structure data
Related structure data | 4ll5C 4lm5C 4ludC 4lueC 3umwS C: citing same article (ref.) 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: 34187.727 Da / Num. of mol.: 1 / Fragment: UNP residues 120-404 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pCR2.1-TOPO / Production host: Escherichia coli (E. coli) References: UniProt: P11309, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-QUE / |
#3: Chemical | ChemComp-GOL / |
#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: 3.23 Å3/Da / Density % sol: 61.9 % / Mosaicity: 0.18 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100MM CITRATE BUFFER PH 5.5, 200MM REMARK 280 NACL, 1M NH4HPO4. Co-crystallised in the presence of 2mM SKF86002. Then these crystals were soaked with 2mM inhibitor dissolved in DMSO., VAPOR ...Details: 100MM CITRATE BUFFER PH 5.5, 200MM REMARK 280 NACL, 1M NH4HPO4. Co-crystallised in the presence of 2mM SKF86002. Then these crystals were soaked with 2mM inhibitor dissolved in DMSO., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 30, 2012 Details: Fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.981→85.191 Å / Num. obs: 17553 / % possible obs: 100 % / Redundancy: 5.1 % / Rsym value: 0.073 / Net I/σ(I): 14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UMW Resolution: 2.38→48.71 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 21.55 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.9 Å2 / Biso mean: 57.1411 Å2 / Biso min: 31.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→48.71 Å
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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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