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- PDB-1uu8: Structure of human PDK1 kinase domain in complex with BIM-1 -

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Basic information

Entry
Database: PDB / ID: 1uu8
TitleStructure of human PDK1 kinase domain in complex with BIM-1
Components3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1
KeywordsTRANSFERASE / PROTEIN KINASE / PKB / PDK1 / INHIBITOR / LY333531 / BISINDOLYL MALEIMIDE / BIM-1 / DIABETES / CANCER / SERINE/THREONINE-PROTEIN KINASE
Function / homology
Function and homology information


Role of LAT2/NTAL/LAB on calcium mobilization / G beta:gamma signalling through PI3Kgamma / GPVI-mediated activation cascade / CD28 dependent PI3K/Akt signaling / FCERI mediated NF-kB activation / Integrin alphaIIb beta3 signaling / RHO GTPases activate PKNs / Regulation of TP53 Degradation / PIP3 activates AKT signaling / Estrogen-stimulated signaling through PRKCZ ...Role of LAT2/NTAL/LAB on calcium mobilization / G beta:gamma signalling through PI3Kgamma / GPVI-mediated activation cascade / CD28 dependent PI3K/Akt signaling / FCERI mediated NF-kB activation / Integrin alphaIIb beta3 signaling / RHO GTPases activate PKNs / Regulation of TP53 Degradation / PIP3 activates AKT signaling / Estrogen-stimulated signaling through PRKCZ / Activation of AKT2 / RSK activation / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / CLEC7A (Dectin-1) signaling / Downstream TCR signaling / Constitutive Signaling by AKT1 E17K in Cancer / 3-phosphoinositide-dependent protein kinase activity / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / phospholipase activator activity / regulation of I-kappaB kinase/NF-kappaB signaling / positive regulation of phospholipase activity / hyperosmotic response / focal adhesion assembly / cellular response to brain-derived neurotrophic factor stimulus / phospholipase binding / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process / positive regulation of sprouting angiogenesis / negative regulation of endothelial cell apoptotic process / extrinsic apoptotic signaling pathway / positive regulation of blood vessel endothelial cell migration / cell projection / negative regulation of protein kinase activity / calcium-mediated signaling / cellular response to epidermal growth factor stimulus / positive regulation of release of sequestered calcium ion into cytosol / T cell costimulation / activation of protein kinase B activity / positive regulation of protein localization to plasma membrane / actin cytoskeleton organization / epidermal growth factor receptor signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / insulin receptor binding / stimulatory C-type lectin receptor signaling pathway / cellular response to insulin stimulus / positive regulation of angiogenesis / Fc-epsilon receptor signaling pathway / platelet activation / peptidyl-threonine phosphorylation / cell migration / cytoplasmic vesicle / T cell receptor signaling pathway / perikaryon / negative regulation of neuron apoptotic process / peptidyl-serine phosphorylation / postsynaptic density / non-specific serine/threonine protein kinase / intracellular signal transduction / protein autophosphorylation / focal adhesion / protein serine/threonine kinase activity / protein phosphorylation / protein kinase binding / ATP binding / plasma membrane / nucleus / cytosol / cytoplasm
Protein kinase, ATP binding site / Serine/Threonine protein kinases active-site signature. / Protein kinases ATP-binding region signature. / Protein kinase domain / PDPK1 family / PDK1-type, PH domain / PH-like domain superfamily / Protein kinase-like domain superfamily / Serine/threonine-protein kinase, active site / Protein kinase domain ...Protein kinase, ATP binding site / Serine/Threonine protein kinases active-site signature. / Protein kinases ATP-binding region signature. / Protein kinase domain / PDPK1 family / PDK1-type, PH domain / PH-like domain superfamily / Protein kinase-like domain superfamily / Serine/threonine-protein kinase, active site / Protein kinase domain / Protein kinase domain profile. / PH domain
3-phosphoinositide-dependent protein kinase 1
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKomander, 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.
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionDec 16, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,84412
Polymers35,4991
Non-polymers1,34511
Water84747
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)122.397, 122.397, 48.016
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2035-

HOH

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Components

#1: Protein/peptide 3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 / HPDK1


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
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Glycerol
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Sulfate
#4: Chemical ChemComp-BI1 / 3-{1-[3-(DIMETHYLAMINO)PROPYL]-1H-INDOL-3-YL}-4-(1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE / RBT205 INHIBITOR


Mass: 412.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H24N4O2 / Bisindolylmaleimide
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58 %
Crystal growpH: 7.5 / Details: 2.1 M AMMONIUM SULPHATE, 0.1 M TRIS-HCL PH 7.50
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-IDDetails
12.1 Mammonium sulfatereservoir
20.1 MTris-HClreservoirpH7.5
310 mMethanoldrop
46.6 mg/mlproteindrop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 13556 / % possible obs: 92.6 % / Redundancy: 3 % / Biso Wilson estimate: 50.9 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2 / % possible all: 75.6
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Redundancy: 3 % / Num. measured all: 40461 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 75.6 % / Redundancy: 2.6 % / Num. unique obs: 1105 / Num. measured obs: 2832 / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H1W
Resolution: 2.5→24.32 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 MODELED AS ALANINE DUE TO DISORDER.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 547 4 %RANDOM
Rwork0.198 ---
Obs0.17642 13551 99.9 %-
Displacement parametersBiso mean: 43.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å2-0.59 Å20 Å2
2--3.19 Å20 Å2
3----6.37 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 88 47 2356
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.199
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.01
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.72

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