+Open data
-Basic information
Entry | Database: PDB / ID: 3orz | ||||||
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Title | PDK1 mutant bound to allosteric disulfide fragment activator 2A2 | ||||||
Components | 3-phosphoinositide-dependent protein kinase 1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE ACTIVATOR / C helix / Ser/Thr-kinase / AGC kinase / allostery / transferase / allosteric activator / bisindolylmaleimide / disulfide / kinase / PDK1 / TRANSFERASE-TRANSFERASE ACTIVATOR complex | ||||||
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 / hyperosmotic response / RSK activation / 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 / hyperosmotic response / RSK activation / 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 / cellular response to epidermal growth factor stimulus / 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 / T cell costimulation / activation of protein kinase B activity / positive regulation of protein localization to plasma membrane / Integrin signaling / insulin-like growth factor receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / negative regulation of transforming growth factor beta receptor signaling pathway / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / epidermal growth factor receptor signaling pathway / cell projection / peptidyl-threonine phosphorylation / calcium-mediated signaling / negative regulation of protein kinase activity / cellular response to insulin stimulus / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Regulation of TP53 Degradation / G beta:gamma signalling through PI3Kgamma / positive regulation of angiogenesis / PIP3 activates AKT signaling / cell migration / Downstream TCR signaling / insulin receptor signaling pathway / actin cytoskeleton organization / cytoplasmic vesicle / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynaptic density / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9995 Å | ||||||
Authors | Sadowsky, J.D. / Wells, J.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Turning a protein kinase on or off from a single allosteric site via disulfide trapping. Authors: Sadowsky, J.D. / Burlingame, M.A. / Wolan, D.W. / McClendon, C.L. / Jacobson, M.P. / 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 | 3orz.cif.gz | 257.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3orz.ent.gz | 204.5 KB | Display | PDB format |
PDBx/mmJSON format | 3orz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3orz_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 3orz_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 3orz_validation.xml.gz | 54.1 KB | Display | |
Data in CIF | 3orz_validation.cif.gz | 74.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/3orz ftp://data.pdbj.org/pub/pdb/validation_reports/or/3orz | HTTPS FTP |
-Related structure data
Related structure data | 3orxC 3otuC 1h1wS 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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Unit cell |
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-Components
#1: Protein | Mass: 36177.457 Da / Num. of mol.: 4 / Fragment: Catalytic domain (UNP residues 51-359) / Mutation: T148C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDK1, PDPK1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 References: UniProt: O15530, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-2A2 / #3: Chemical | ChemComp-BI4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 1.8M ammonium sulfate, 0.1M potassium tartrate, 0.1M sodium citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11588 Å / Relative weight: 1 |
Reflection | Resolution: 1.999→50 Å / Num. all: 69773 / Num. obs: 69773 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.65 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 20.456 |
Reflection shell | Resolution: 1.999→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3.784 / Num. unique all: 3432 / Rsym value: 0.273 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H1W Resolution: 1.9995→41.985 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 46.34 / 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 / Bsol: 41.493 Å2 / ksol: 0.383 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9995→41.985 Å
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Refine LS restraints |
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LS refinement shell |
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