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- PDB-8dqt: Human PDK1 kinase domain in complex with Valsartan -

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Basic information

Entry
Database: PDB / ID: 8dqt
TitleHuman PDK1 kinase domain in complex with Valsartan
Components3-phosphoinositide-dependent protein kinase 1
KeywordsTRANSFERASE / AGC KINASE / PHOSPHORYLATION / PDK1 / PIF-POCKET / ALPHA-C HELIX / PHOSPHOPROTEIN / SERINE/THREONINE-PROTEIN KINASE / KINASE TRANSFERASE
Function / homology
Function and homology information


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 / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process ...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 / 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 / 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 / vascular endothelial cell response to laminar fluid shear stress / negative regulation of endothelial cell apoptotic process / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / activation of protein kinase B activity / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / GPVI-mediated activation cascade / extrinsic apoptotic signaling pathway / T cell costimulation / Integrin signaling / peptidyl-threonine phosphorylation / cellular response to epidermal growth factor stimulus / insulin-like growth factor receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / cell projection / positive regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transforming growth factor beta receptor signaling pathway / calcium-mediated signaling / CLEC7A (Dectin-1) signaling / epidermal growth factor receptor signaling pathway / FCERI mediated NF-kB activation / cellular response to insulin stimulus / positive regulation of angiogenesis / G beta:gamma signalling through PI3Kgamma / Regulation of TP53 Degradation / insulin receptor signaling pathway / Downstream TCR signaling / cell migration / PIP3 activates AKT signaling / actin cytoskeleton organization / protein autophosphorylation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / cytoplasmic vesicle / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / postsynaptic density / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PDK1-type, PH domain / PH domain / PDPK1 family / : / PH-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...PDK1-type, PH domain / PH domain / PDPK1 family / : / PH-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-U35 / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsGross, L.Z.F. / Klinke, S. / Biondi, R.M.
Funding support Argentina, 1items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT 2016-3525 Argentina
CitationJournal: Sci.Signal. / Year: 2023
Title: Modulation of the substrate specificity of the kinase PDK1 by distinct conformations of the full-length protein.
Authors: Sacerdoti, M. / Gross, L.Z.F. / Riley, A.M. / Zehnder, K. / Ghode, A. / Klinke, S. / Anand, G.S. / Paris, K. / Winkel, A. / Herbrand, A.K. / Godage, H.Y. / Cozier, G.E. / Suss, E. / Schulze, ...Authors: Sacerdoti, M. / Gross, L.Z.F. / Riley, A.M. / Zehnder, K. / Ghode, A. / Klinke, S. / Anand, G.S. / Paris, K. / Winkel, A. / Herbrand, A.K. / Godage, H.Y. / Cozier, G.E. / Suss, E. / Schulze, J.O. / Pastor-Flores, D. / Bollini, M. / Cappellari, M.V. / Svergun, D. / Grawert, M.A. / Aramendia, P.F. / Leroux, A.E. / Potter, B.V.L. / Camacho, C.J. / Biondi, R.M.
History
DepositionJul 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)36,7915
Polymers35,3931
Non-polymers1,3994
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.510, 44.590, 48.210
Angle α, β, γ (deg.)90.000, 101.320, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein 3-phosphoinositide-dependent protein kinase 1 / hPDK1


Mass: 35392.566 Da / Num. of mol.: 1 / Mutation: Y288G, Q292A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDPK1, PDK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O15530, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-U35 / (2~{S})-3-methyl-2-[pentanoyl-[[4-[2-(2~{H}-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]methyl]amino]butanoic acid / (2~{S})-3-methyl-2-[pentanoyl-[[4-[2-(2~{H}-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]methyl]amino]butanoic acid / Diovan / Tareg / Provas / Exforge / N-(p-(o-1H-Tetrazol-5-ylphenyl)benzyl)-N-valeryl-L-valine


Mass: 435.519 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H29N5O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.61 % / Description: Bipyramids
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.2M sodium citrate, 0.1M Hepes pH 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2019
Details: CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.31→47.27 Å / Num. obs: 73419 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.37 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.055 / Net I/σ(I): 15.9
Reflection shellResolution: 1.31→1.39 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 11539 / CC1/2: 0.744 / Rrim(I) all: 1.306 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
MxCuBEdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HRC

3hrc


Resolution: 1.31→36.51 Å / SU ML: 0.1982 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4433
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2242 3664 5 %
Rwork0.1991 69636 -
obs0.2004 73300 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.98 Å2
Refinement stepCycle: LAST / Resolution: 1.31→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 0 133 2590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00952521
X-RAY DIFFRACTIONf_angle_d1.10873403
X-RAY DIFFRACTIONf_chiral_restr0.0966355
X-RAY DIFFRACTIONf_plane_restr0.0084431
X-RAY DIFFRACTIONf_dihedral_angle_d20.3682343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.330.38861220.37822320X-RAY DIFFRACTION88.38
1.33-1.350.36071420.35762705X-RAY DIFFRACTION99.44
1.35-1.370.38151400.34712645X-RAY DIFFRACTION99.46
1.37-1.390.36621420.33692694X-RAY DIFFRACTION99.61
1.39-1.410.35361410.3282673X-RAY DIFFRACTION99.61
1.41-1.430.3781410.3172690X-RAY DIFFRACTION99.61
1.43-1.460.36151380.32142653X-RAY DIFFRACTION99.54
1.46-1.490.3491410.33492661X-RAY DIFFRACTION99.61
1.49-1.510.35161430.32342704X-RAY DIFFRACTION99.55
1.51-1.540.32151390.27272650X-RAY DIFFRACTION99.75
1.54-1.580.31411410.25922667X-RAY DIFFRACTION99.93
1.58-1.610.32251420.23962710X-RAY DIFFRACTION99.96
1.61-1.660.24441410.22262678X-RAY DIFFRACTION99.89
1.66-1.70.22861420.20482696X-RAY DIFFRACTION99.89
1.7-1.750.24231400.19742653X-RAY DIFFRACTION99.75
1.75-1.810.19751410.19582697X-RAY DIFFRACTION99.68
1.81-1.870.2231420.19492691X-RAY DIFFRACTION99.58
1.87-1.950.18641420.17962698X-RAY DIFFRACTION99.79
1.95-2.030.19121410.17952689X-RAY DIFFRACTION99.37
2.03-2.140.22781410.18192681X-RAY DIFFRACTION99.68
2.14-2.280.21461420.18262701X-RAY DIFFRACTION99.93
2.28-2.450.20781430.19592709X-RAY DIFFRACTION99.79
2.45-2.70.21921420.19612706X-RAY DIFFRACTION99.75
2.7-3.090.20871440.19612729X-RAY DIFFRACTION99.58
3.09-3.890.20211440.17662728X-RAY DIFFRACTION99.83
3.89-36.510.19681470.17022808X-RAY DIFFRACTION99.53

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