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- PDB-4rrv: Crystal structure of PDK1 in complex with ATP and PIFtide -

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Basic information

Entry
Database: PDB / ID: 4rrv
TitleCrystal structure of PDK1 in complex with ATP and PIFtide
Components
  • 3-phosphoinositide-dependent protein kinase 1
  • Serine/threonine-protein kinase N2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / PIFtide / phosphorylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


epithelial cell migration / intracellular signaling cassette / Activation of AKT2 / protein kinase C / regulation of mast cell degranulation / diacylglycerol-dependent serine/threonine kinase activity / type B pancreatic cell development / negative regulation of toll-like receptor signaling pathway / regulation of cell motility / apical junction assembly ...epithelial cell migration / intracellular signaling cassette / Activation of AKT2 / protein kinase C / regulation of mast cell degranulation / diacylglycerol-dependent serine/threonine kinase activity / type B pancreatic cell development / negative regulation of toll-like receptor signaling pathway / regulation of cell motility / apical junction assembly / cell projection organization / intermediate filament cytoskeleton / RSK activation / RNA polymerase binding / regulation of canonical NF-kappaB signal transduction / hyperosmotic response / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process / phospholipase activator activity / apical junction complex / RHOB GTPase cycle / positive regulation of cytokinesis / RHOC GTPase cycle / positive regulation of sprouting angiogenesis / Constitutive Signaling by AKT1 E17K in Cancer / cleavage furrow / RHOA GTPase cycle / CD28 dependent PI3K/Akt signaling / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of endothelial cell apoptotic process / Estrogen-stimulated signaling through PRKCZ / vascular endothelial cell response to laminar fluid shear stress / positive regulation of viral genome replication / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / phospholipase binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / GPVI-mediated activation cascade / RHO GTPases activate PKNs / T cell costimulation / extrinsic apoptotic signaling pathway / RAC1 GTPase cycle / Integrin signaling / positive regulation of mitotic cell cycle / insulin-like growth factor receptor signaling pathway / cellular response to epidermal growth factor stimulus / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / cell projection / 3-phosphoinositide-dependent protein kinase activity / 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 / small GTPase binding / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / histone deacetylase binding / cellular response to insulin stimulus / epidermal growth factor receptor signaling pathway / positive regulation of angiogenesis / G beta:gamma signalling through PI3Kgamma / kinase activity / Regulation of TP53 Degradation / insulin receptor signaling pathway / Downstream TCR signaling / cell migration / PIP3 activates AKT signaling / lamellipodium / actin cytoskeleton organization / protein autophosphorylation / midbody / cytoplasmic vesicle / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / cell adhesion / postsynaptic density / intracellular signal transduction / nuclear body / protein phosphorylation / cadherin binding / cell division / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / centrosome / perinuclear region of cytoplasm / signal transduction / protein-containing complex / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Serine/threonine-protein kinase N, first HR1 domain / Serine/threonine-protein kinase N, C2 domain / Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / PDK1-type, PH domain / PH domain / PDPK1 family / HR1 rho-binding domain / REM-1 domain profile. ...Serine/threonine-protein kinase N, first HR1 domain / Serine/threonine-protein kinase N, C2 domain / Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / PDK1-type, PH domain / PH domain / PDPK1 family / HR1 rho-binding domain / REM-1 domain profile. / : / Protein kinase, C-terminal / Protein kinase C terminal domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / PH-like domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / 3-phosphoinositide-dependent protein kinase 1 / Serine/threonine-protein kinase N2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.412 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 6, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: Serine/threonine-protein kinase N2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0795
Polymers37,3882
Non-polymers6913
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-9 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.973, 44.536, 47.799
Angle α, β, γ (deg.)90.000, 101.400, 90.000
Int Tables number5
Space group name H-MC121

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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: Protein/peptide Serine/threonine-protein kinase N2 / PKN gamma / Protein kinase C-like 2 / Protein-kinase C-related kinase 2


Mass: 1995.105 Da / Num. of mol.: 1
Fragment: PIFtide (PRK2 hydrophobic motif, UNP residues 969-983)
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16513
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.83 %
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: 1.41→50 Å / Num. all: 59080 / Num. obs: 58388 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 13.81 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.141 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.41-1.462.60.83253541.171191.5
1.46-1.523.50.6258561.197199.7
1.52-1.593.60.42658991.178199.9
1.59-1.673.60.31158391.18199.8
1.67-1.783.60.20858751.156199.9
1.78-1.913.70.13558811.181199.7
1.91-2.113.70.08158741.118199.6
2.11-2.413.60.0658721.025199.5
2.41-3.043.50.05659131.107199.5
3.04-503.50.02560251.111199.1

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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: 1.412→46.855 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 16.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1632 2947 5.05 %RANDOM
Rwork0.1336 ---
obs0.1351 58384 --
all-58386 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.35 Å2 / Biso mean: 21.8376 Å2 / Biso min: 6.03 Å2
Refinement stepCycle: LAST / Resolution: 1.412→46.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 43 297 2716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092606
X-RAY DIFFRACTIONf_angle_d1.3263537
X-RAY DIFFRACTIONf_chiral_restr0.08382
X-RAY DIFFRACTIONf_plane_restr0.008442
X-RAY DIFFRACTIONf_dihedral_angle_d13.9891001
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.412-1.43560.32241170.25972272238986
1.4356-1.46040.28891220.23652502262495
1.4604-1.4870.2771340.20392693282799
1.487-1.51560.21211390.179926102749100
1.5156-1.54650.2031380.163726722810100
1.5465-1.58010.19771390.150626722811100
1.5801-1.61690.20031480.140826252773100
1.6169-1.65730.21251500.135226692819100
1.6573-1.70210.1841380.134126542792100
1.7021-1.75220.16621460.124126322778100
1.7522-1.80880.16711460.11626642810100
1.8088-1.87340.19111460.119326452791100
1.8734-1.94840.13821430.110226772820100
1.9484-2.03710.1531470.102926432790100
2.0371-2.14450.12031460.103826452791100
2.1445-2.27890.15081500.106826752825100
2.2789-2.45480.13781420.1142657279999
2.4548-2.70180.17321280.129526832811100
2.7018-3.09270.16521370.13626922829100
3.0927-3.89620.16011430.12882707285099
3.8962-46.88110.13791480.15222748289699

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