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Yorodumi- PDB-3hrf: Crystal structure of Human PDK1 kinase domain in complex with an ... -
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-Basic information
Entry | Database: PDB / ID: 3hrf | ||||||
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Title | Crystal structure of Human PDK1 kinase domain in complex with an allosteric activator bound to the PIF-pocket | ||||||
Components | 3-phosphoinositide-dependent protein kinase 1 | ||||||
Keywords | TRANSFERASE / AGC KINASE / PHOSPHORYLATION / ALLOSTERY / PDK1 / PIF-POCKET / ALPHA-C HELIX / ACTIVATION LOOP / ATP BINDING / ATP-binding / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase | ||||||
Function / homology | Function and homology information 3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / positive regulation of vascular endothelial cell proliferation ...3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process / phospholipase activator activity / positive regulation of sprouting angiogenesis / Constitutive Signaling by AKT1 E17K in Cancer / CD28 dependent PI3K/Akt signaling / phospholipase binding / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / Estrogen-stimulated signaling through PRKCZ / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of endothelial cell apoptotic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway / RHO GTPases activate PKNs / GPVI-mediated activation cascade / cellular response to epidermal growth factor stimulus / T cell costimulation / activation of protein kinase B activity / Integrin signaling / insulin-like growth factor receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / cell projection / calcium-mediated signaling / positive regulation of protein localization to plasma membrane / negative regulation of transforming growth factor beta receptor signaling pathway / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / epidermal growth factor receptor signaling pathway / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / G beta:gamma signalling through PI3Kgamma / cellular response to insulin stimulus / positive regulation of angiogenesis / Regulation of TP53 Degradation / cell migration / Downstream TCR signaling / PIP3 activates AKT signaling / insulin receptor signaling pathway / cytoplasmic vesicle / actin cytoskeleton organization / protein autophosphorylation / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hindie, V. / Alzari, P.M. / Biondi, R.M. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2009 Title: Structure and allosteric effects of low-molecular-weight activators on the protein kinase PDK1. Authors: Hindie, V. / Stroba, A. / Zhang, H. / Lopez-Garcia, L.A. / Idrissova, L. / Zeuzem, S. / Hirschberg, D. / Schaeffer, F. / Jrgensen, T.J. / Engel, M. / Alzari, P.M. / Biondi, R.M. #1: Journal: To be Published Title: 3,5-diphenyl pent-2-enoic acids as allosteric activators of the protein kinase PDK1: Structure-activity relationships and thermodynamic characterisation of binding as a paradigm for PIF- ...Title: 3,5-diphenyl pent-2-enoic acids as allosteric activators of the protein kinase PDK1: Structure-activity relationships and thermodynamic characterisation of binding as a paradigm for PIF-binding pocket-targeting compounds Authors: Stroba, A. / Schaeffer, F. / Hindie, V. / Lopez-Garcia, L.A. / Frohner, W. / Adrian, I. / Hartmann, R.W. / Biondi, R.M. / Engel, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hrf.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hrf.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 3hrf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/3hrf ftp://data.pdbj.org/pub/pdb/validation_reports/hr/3hrf | HTTPS FTP |
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-Related structure data
Related structure data | 3hrcSC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 35392.566 Da / Num. of mol.: 1 / Fragment: PDK1 KINASE DOMAIN / Mutation: Y288G, Q292A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Gene: PDK1, PDPK1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15530 | ||||
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#2: Chemical | ChemComp-ATP / | ||||
#3: Chemical | ChemComp-P47 / ( | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | GLY49 AND ALA50 ARE FROM TEV CLEAVAGE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.4M SODIUM CITRATE, 0.1M SODIUM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2007 |
Radiation | Monochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.47 Å / Num. all: 23875 / Num. obs: 23875 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 16.22 Å2 / Rmerge(I) obs: 0.094 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3464 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HRC Resolution: 1.9→46.47 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.132 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.137 / ESU R Free: 0.111 / 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 max: 57.96 Å2 / Biso mean: 13.846 Å2 / Biso min: 3.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→46.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 24.147 Å / Origin y: -22.753 Å / Origin z: -25.525 Å
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Refinement TLS group |
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