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Yorodumi- PDB-1w1d: Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w1d | ||||||
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Title | Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to Inositol (1,3,4,5)-tetrakisphosphate | ||||||
Components | 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 | ||||||
Keywords | TRANSFERASE / PDK1 / PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1 / PKB / PLECKSTRIN HOMOLOGY DOMAIN / INOSITOL PHOSPHATE / PHOSPHOINOSITIDE / SIGNAL TRANSDUCTION / PI3-KINASE / 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 / negative regulation of cardiac muscle cell apoptotic process ...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 / negative regulation of cardiac muscle cell apoptotic process / positive regulation of vascular endothelial cell proliferation / phospholipase activator activity / positive regulation of sprouting angiogenesis / Constitutive Signaling by AKT1 E17K in Cancer / phospholipase binding / CD28 dependent PI3K/Akt signaling / 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 / cellular response to epidermal growth factor stimulus / GPVI-mediated activation cascade / T cell costimulation / activation of protein kinase B activity / 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 / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / G beta:gamma signalling through PI3Kgamma / cellular response to insulin stimulus / positive regulation of angiogenesis / cell migration / Regulation of TP53 Degradation / Downstream TCR signaling / PIP3 activates AKT signaling / insulin receptor signaling pathway / cytoplasmic vesicle / actin cytoskeleton organization / postsynaptic density / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / focal adhesion / protein serine kinase activity / 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 / MAD / Resolution: 1.5 Å | ||||||
Authors | Komander, D. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F. | ||||||
Citation | Journal: Embo J. / Year: 2004 Title: Structural Insights Into the Regulation of Pdk1 by Phosphoinositides and Inositol Phosphates Authors: Komander, D. / Fairservice, A. / Deak, M. / Kular, G.S. / Prescott, A.R. / Downes, C.P. / Safrany, S.T. / Alessi, D.R. / Van Aalten, D.M.F. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Purification, Crystallisation and Preliminary X-Ray Difffraction of a Proteolytic Fragment of Pdk1, Containing the Pleckstrin Homology Domain Authors: Komander, D. / Deak, M. / Morrice, N. / Van Aalten, D.M.F. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w1d.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w1d.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 1w1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/1w1d ftp://data.pdbj.org/pub/pdb/validation_reports/w1/1w1d | 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: 17816.186 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 409-556 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O15530, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-AU / |
#4: Chemical | ChemComp-4IP / |
#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: 2.1 Å3/Da / Density % sol: 0.41 % |
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Crystal grow | Details: 0.08 M MAGNESIUM ACETATE, 0.05M SODIUM CACODYLATE PH 6.5, 30 % PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.861,1.040 | |||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: May 5, 2003 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→25 Å / Num. obs: 23341 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.7 | |||||||||
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.332 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE CHAINS OF SOME DISORDERED RESIDUES WERE REFINED EITHER WITH THE OCCUPANCY SET TO 0.02, OR THE RESIDUE WAS MUTATED TO ALA.
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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: 13.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→25 Å
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