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- PDB-3nuy: phosphoinositide-dependent kinase-1 (PDK1) with fragment17 -

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Basic information

Entry
Database: PDB / ID: 3nuy
Titlephosphoinositide-dependent kinase-1 (PDK1) with fragment17
ComponentsPkB-likePyruvate dehydrogenase lipoamide kinase isozyme 1
KeywordsTRANSFERASE / Kinase domain
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
PDK1-type, PH domain / PDPK1 family / PH domain / PH-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...PDK1-type, PH domain / PDPK1 family / PH domain / PH-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
quinazolin-4(1H)-one / 3-phosphoinositide-dependent protein kinase 1 / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsCampobasso, N. / Ward, P.
CitationJournal: ACS Med Chem Lett / Year: 2010
Title: Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery.
Authors: Medina, J.R. / Blackledge, C.W. / Heerding, D.A. / Campobasso, N. / Ward, P. / Briand, J. / Wright, L. / Axten, J.M.
History
DepositionJul 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 30, 2016Group: Other
Revision 1.3Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PkB-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9109
Polymers33,1081
Non-polymers8038
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PkB-like
hetero molecules

A: PkB-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,82118
Polymers66,2162
Non-polymers1,60516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4530 Å2
ΔGint-89 kcal/mol
Surface area25050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.695, 123.695, 47.346
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PkB-like / Pyruvate dehydrogenase lipoamide kinase isozyme 1


Mass: 33107.754 Da / Num. of mol.: 1 / Fragment: UNP residues 65-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PkB-like 1 / Production host: Baculovirus / References: UniProt: Q9UPJ8, UniProt: O15530*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-JPZ / quinazolin-4(1H)-one


Mass: 146.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6N2O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 K / Method: sitting drop / pH: 9
Details: 2M Ammonium sulfate, 0.1M TRIS, pH 9, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1.0786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0786 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 24014 / % possible obs: 97 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.064 / Χ2: 1.003 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.186.60.52324221.011198.3
2.18-2.266.70.37424141.008198.2
2.26-2.376.70.28324051.002198.5
2.37-2.496.70.21923810.996198
2.49-2.656.80.17624261.007197.8
2.65-2.856.80.11723851.009198.1
2.85-3.146.80.08124071.009196.8
3.14-3.596.80.06423900.992196.6
3.59-4.526.90.04123820.993195.6
4.52-506.80.03424021.007192.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.489 Å / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.8671 / SU ML: 0.26 / σ(F): 0.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 1923 8.34 %
Rwork0.1832 --
obs0.1866 23064 93.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.58 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 86.87 Å2 / Biso mean: 37.7667 Å2 / Biso min: 19.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.4523 Å20 Å2-0 Å2
2--0.4523 Å2-0 Å2
3----0.9046 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 50 69 2362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122385
X-RAY DIFFRACTIONf_angle_d1.3623192
X-RAY DIFFRACTIONf_chiral_restr0.092343
X-RAY DIFFRACTIONf_plane_restr0.007399
X-RAY DIFFRACTIONf_dihedral_angle_d15.519859
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14640.25331250.20661382150786
2.1464-2.20440.23911360.18241437157391
2.2044-2.26930.24181370.18341429156689
2.2693-2.34250.23931370.18191488162593
2.3425-2.42620.24761320.17821488162093
2.4262-2.52340.22921410.17971500164192
2.5234-2.63820.2461370.1931516165394
2.6382-2.77720.23571380.20111530166895
2.7772-2.95120.25241360.19961559169596
2.9512-3.1790.26291460.19921558170496
3.179-3.49870.23881430.18641547169097
3.4987-4.00460.17081390.15571573171295
4.0046-5.04390.18041370.15081561169895
5.0439-40.49620.2351390.19161573171292

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