+Open data
-Basic information
Entry | Database: PDB / ID: 4rrv | ||||||
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Title | Crystal structure of PDK1 in complex with ATP and PIFtide | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / PIFtide / phosphorylation / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information epithelial cell migration / 3-phosphoinositide-dependent protein kinase activity / protein kinase C / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / diacylglycerol-dependent serine/threonine kinase activity / type B pancreatic cell development / cell projection organization / positive regulation of phospholipase activity ...epithelial cell migration / 3-phosphoinositide-dependent protein kinase activity / protein kinase C / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / diacylglycerol-dependent serine/threonine kinase activity / type B pancreatic cell development / cell projection organization / positive regulation of phospholipase activity / apical junction assembly / RSK activation / hyperosmotic response / regulation of cell motility / RNA polymerase binding / regulation of canonical NF-kappaB signal transduction / negative regulation of cardiac muscle cell apoptotic process / intermediate filament cytoskeleton / positive regulation of vascular endothelial cell proliferation / apical junction complex / RHOB GTPase cycle / phospholipase activator activity / positive regulation of sprouting angiogenesis / RHOC GTPase cycle / positive regulation of cytokinesis / Constitutive Signaling by AKT1 E17K in Cancer / cleavage furrow / phospholipase binding / CD28 dependent PI3K/Akt signaling / RHOA GTPase cycle / positive regulation of blood vessel endothelial cell migration / positive regulation of viral genome replication / 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 / cellular response to epidermal growth factor stimulus / GPVI-mediated activation cascade / RAC1 GTPase cycle / T cell costimulation / activation of protein kinase B activity / positive regulation of mitotic cell cycle / Integrin signaling / positive regulation of release of sequestered calcium ion into cytosol / insulin-like growth factor receptor signaling pathway / 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 / small GTPase binding / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / G beta:gamma signalling through PI3Kgamma / histone deacetylase binding / cellular response to insulin stimulus / positive regulation of angiogenesis / cell migration / Regulation of TP53 Degradation / Downstream TCR signaling / PIP3 activates AKT signaling / lamellipodium / insulin receptor signaling pathway / kinase activity / midbody / cytoplasmic vesicle / actin cytoskeleton organization / postsynaptic density / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / nuclear body / non-specific serine/threonine protein kinase / cell adhesion / protein kinase activity / intracellular signal transduction / cadherin binding / cell cycle / cell division / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / perinuclear region of cytoplasm / signal transduction / protein-containing complex / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.412 Å | ||||||
Authors | Rettenmaier, T.J. / Wells, J.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1. Authors: Rettenmaier, T.J. / Sadowsky, J.D. / Thomsen, N.D. / Chen, S.C. / Doak, A.K. / Arkin, M.R. / Wells, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rrv.cif.gz | 203.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rrv.ent.gz | 163.2 KB | Display | PDB format |
PDBx/mmJSON format | 4rrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rr/4rrv ftp://data.pdbj.org/pub/pdb/validation_reports/rr/4rrv | HTTPS FTP |
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-Related structure data
Related structure data | 4rqkC 4rqvC 4aw1S 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: 35392.566 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 50-359) / Mutation: Y288G Q292A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDK1, PDPK1 / Plasmid: pFastBac HTB / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 References: UniProt: O15530, non-specific serine/threonine protein kinase | ||
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#2: Protein/peptide | Mass: 1995.105 Da / Num. of mol.: 1 Fragment: PIFtide (PRK2 hydrophobic motif, UNP residues 969-983) Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16513 | ||
#3: Chemical | ChemComp-ATP / | ||
#4: Chemical | #5: 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: 2.08 Å3/Da / Density % sol: 40.83 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 21 mg/mL protein in 25 mM Tris, pH 7.5, 0.5 M sodium chloride, 1 mM DTT, 15 mM EDTA, 15 mM ATP, precipitant: 0.1 M HEPES, pH 7.5, 1.2 M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.41→50 Å / Num. all: 59080 / Num. obs: 58388 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 13.81 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.141 / Net I/σ(I): 13.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AW1 Resolution: 1.412→46.855 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 16.19 / 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: 88.35 Å2 / Biso mean: 21.8376 Å2 / Biso min: 6.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.412→46.855 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21
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