+Open data
-Basic information
Entry | Database: PDB / ID: 1uvr | ||||||
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Title | Structure of human PDK1 kinase domain in complex with BIM-8 | ||||||
Components | 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 | ||||||
Keywords | TRANSFERASE / PROTEIN KINASE / PKB / PDK1 / INHIBITOR / LY333531 / BISINDOLYL MALEIMIDE / BIM-8 / DIABETES / CANCER | ||||||
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: 2.81 Å | ||||||
Authors | Komander, D. / Garrido-Franco, M. / Kular, G.S. / Schuttelkopf, A.W. / Deak, M. / Prakash, K.R. / Bain, J. / Elliot, 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 | 1uvr.cif.gz | 76.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uvr.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 1uvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uvr_validation.pdf.gz | 861.1 KB | Display | wwPDB validaton report |
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Full document | 1uvr_full_validation.pdf.gz | 869.2 KB | Display | |
Data in XML | 1uvr_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 1uvr_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/1uvr ftp://data.pdbj.org/pub/pdb/validation_reports/uv/1uvr | HTTPS FTP |
-Related structure data
Related structure data | 1uu3C 1uu7C 1uu8C 1uu9C 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
#1: Protein | Mass: 33452.469 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 71-359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: BACULOVIRUS INFECTED / Cell line: SF21 / 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-SO4 / #4: Chemical | ChemComp-BI8 / | #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: 2.0 M AMMONIUM SULPHATE, 0.1 M TRIS-HCL PH 7.75 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.75 / 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: ID14-1 / Wavelength: 0.934 |
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: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→25 Å / Num. obs: 9493 / % possible obs: 90.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2 / % possible all: 90.3 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 25 Å / Redundancy: 3.5 % / Num. measured all: 32999 / Rmerge(I) obs: 0.138 |
Reflection shell | *PLUS % possible obs: 90.3 % / Redundancy: 3.5 % / Num. unique obs: 915 / Num. measured obs: 3180 / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H1W Resolution: 2.81→23.37 Å / SU B: 4.062 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.152 Details: SOME SIDECHAINS REFINED WITH OCCUPANCY = 0.00 DUE TO DISORDER. SOME RESIDUES MUTATED TO ALANINE DUE TO DISORDER.
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Displacement parameters | Biso mean: 30.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→23.37 Å
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.193 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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