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- PDB-4rqv: Crystal structure of PDK1 in complex with ATP and the PIF-pocket ... -

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Basic information

Entry
Database: PDB / ID: 4rqv
TitleCrystal structure of PDK1 in complex with ATP and the PIF-pocket ligand RS2
Components3-phosphoinositide-dependent protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Protein Kinase / Phosphorylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Estrogen-stimulated signaling through PRKCZ / negative regulation of endothelial cell apoptotic process / 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 / cellular response to epidermal growth factor stimulus / activation of protein kinase B activity / Integrin signaling / insulin-like growth factor receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / cell projection / peptidyl-threonine phosphorylation / positive regulation of protein localization to plasma membrane / calcium-mediated signaling / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein kinase activity / epidermal growth factor receptor signaling pathway / CLEC7A (Dectin-1) signaling / cellular response to insulin stimulus / FCERI mediated NF-kB activation / positive regulation of angiogenesis / G beta:gamma signalling through PI3Kgamma / Regulation of TP53 Degradation / cell migration / Downstream TCR signaling / PIP3 activates AKT signaling / insulin receptor signaling pathway / actin cytoskeleton organization / cytoplasmic vesicle / protein autophosphorylation / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / cytosol / cytoplasm
Similarity search - Function
PDK1-type, PH domain / PH domain / PDPK1 family / : / 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 ...PDK1-type, PH domain / PH domain / PDPK1 family / : / 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
ADENOSINE-5'-TRIPHOSPHATE / Chem-R2S / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å
AuthorsRettenmaier, T.J. / Wells, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1.
Authors: Rettenmaier, T.J. / Sadowsky, J.D. / Thomsen, N.D. / Chen, S.C. / Doak, A.K. / Arkin, M.R. / Wells, J.A.
History
DepositionNov 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6497
Polymers35,3931
Non-polymers1,2566
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.130, 44.480, 47.659
Angle α, β, γ (deg.)90.000, 100.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2311-

HOH

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Components

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


Mass: 35392.566 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 50-359) / Mutation: Y288G, Q292A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDK1, PDPK1 / Plasmid: pFastBac HTB / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: O15530, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-R2S / N-(6-chloro-1,3-benzothiazol-2-yl)-1-benzothiophene-2-sulfonamide


Mass: 380.892 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H9ClN2O2S3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 21 mg/mL protein in 25 mM Tris, pH 7.5, 0.5 M sodium chloride, 1 mM DTT, 15 mM EDTA, 15 mM ATP, precipitant: 0.1 M HEPES, pH 7.5, 1.2 M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2013
RadiationMonochromator: Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 48810 / Num. obs: 46184 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 14.09 Å2 / Rmerge(I) obs: 0.059 / Χ2: 1.097 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.552.40.55631841.13165.8
1.55-1.622.70.4539821.139182.2
1.62-1.693.40.3647651.166198.2
1.69-1.783.60.2648631.1491100
1.78-1.893.70.1848401.1451100
1.89-2.043.70.11248761.051199.9
2.04-2.243.70.07248671.045199.9
2.24-2.563.70.05548771.032199.9
2.56-3.233.60.05149071.133199.9
3.23-503.60.02650231.025199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_1692refinement
PDB_EXTRACT3.15data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AW1

4aw1


Resolution: 1.502→46.843 Å / SU ML: 0.15 / σ(F): 1.37 / Phase error: 16.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1657 2354 5.1 %RANDOM
Rwork0.1315 ---
obs0.1333 46182 --
all-46182 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.45 Å2 / Biso mean: 21.2474 Å2 / Biso min: 6.42 Å2
Refinement stepCycle: LAST / Resolution: 1.502→46.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 78 321 2747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082663
X-RAY DIFFRACTIONf_angle_d1.2923623
X-RAY DIFFRACTIONf_chiral_restr0.048378
X-RAY DIFFRACTIONf_plane_restr0.007449
X-RAY DIFFRACTIONf_dihedral_angle_d24.2821043
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.502-1.53240.2621910.22591648173960
1.5324-1.56570.2645940.19251901199571
1.5657-1.60220.21761140.1722223233781
1.6022-1.64220.21141430.16242507265092
1.6422-1.68660.23841570.147526812838100
1.6866-1.73630.20151360.131327062842100
1.7363-1.79230.19441530.12827102863100
1.7923-1.85640.19131590.12727382897100
1.8564-1.93070.16371450.121927162861100
1.9307-2.01860.17441370.109327262863100
2.0186-2.1250.15181600.1126952855100
2.125-2.25810.13891460.101927442890100
2.2581-2.43250.15011510.108227122863100
2.4325-2.67720.17111300.128227682898100
2.6772-3.06460.15811390.13427512890100
3.0646-3.86080.15521480.127927672915100
3.8608-46.86540.14631510.151928352986100

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