+Open data
-Basic information
Entry | Database: PDB / ID: 1uu7 | ||||||
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Title | Structure of human PDK1 kinase domain in complex with BIM-2 | ||||||
Components | 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 | ||||||
Keywords | TRANSFERASE / PROTEIN KINASE / PKB / PDK1 / INHIBITOR / LY333531 / BISINDOLYL MALEIMIDE / BIM-1 / DIABETES / CANCER / 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 / extrinsic apoptotic signaling pathway / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Komander, D. / Kular, G.S. / Schuttelkopf, A.W. / Deak, M. / Prakash, K.R. / Bain, J. / Elliot, M. / Garrido-Franco, M. / Kozikowski, A.P. / Alessi, D.R. / Van Aalten, D.M.F. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Interactions of Ly333531 and Other Bisindolyl Maleimide Inhibitors with Pdk1 Authors: Komander, D. / Kular, G.S. / Schuttelkopf, A.W. / Deak, M. / Prakash, K.R. / Bain, J. / Elliot, M. / Garrido-Franco, M. / Kozikowski, A.P. / Alessi, D.R. / Van Aalten, D.M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uu7.cif.gz | 81.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uu7.ent.gz | 59.2 KB | Display | PDB format |
PDBx/mmJSON format | 1uu7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/1uu7 ftp://data.pdbj.org/pub/pdb/validation_reports/uu/1uu7 | HTTPS FTP |
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-Related structure data
Related structure data | 1uu3C 1uu8C 1uu9C 1uvrC 1h1wS 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: 35498.688 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 51-360 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: BACULOVIRUS INFECTED / Plasmid: PFASTBAC1 / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O15530, EC: 2.7.1.37 | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-BI2 / | #4: Chemical | ChemComp-SO4 / #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: 3 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 2.3 M AMMONIUM SULPHATE 0.1 M TRIS-HCL PH 8.25 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.25 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 44644 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 25 Å / Num. obs: 32482 / Redundancy: 3.7 % / Num. measured all: 118992 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 99.8 % / Redundancy: 3.5 % / Num. unique obs: 3218 / Num. measured obs: 11353 / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H1W Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.88 / SU B: 4.023 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: SOME SIDECHAINS REFINED WITH OCCUPANCY = 0.00 DUE TO DISORDER. SOME RESIDUES MODELED AS ALANINE DUE TO DISORDER.
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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: 18.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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