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- PDB-1w1d: Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bou... -

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Basic information

Entry
Database: PDB / ID: 1w1d
TitleCrystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to Inositol (1,3,4,5)-tetrakisphosphate
Components3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1
KeywordsTRANSFERASE / PDK1 / PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1 / PKB / PLECKSTRIN HOMOLOGY DOMAIN / INOSITOL PHOSPHATE / PHOSPHOINOSITIDE / SIGNAL TRANSDUCTION / PI3-KINASE / SERINE/THREONINE PROTEIN KINASE
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 / : / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...PDK1-type, PH domain / PH domain / PDPK1 family / : / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / 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 / Mainly Beta
Similarity search - Domain/homology
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / : / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsKomander, D. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
Citation
Journal: Embo J. / Year: 2004
Title: Structural Insights Into the Regulation of Pdk1 by Phosphoinositides and Inositol Phosphates
Authors: Komander, D. / Fairservice, A. / Deak, M. / Kular, G.S. / Prescott, A.R. / Downes, C.P. / Safrany, S.T. / Alessi, D.R. / Van Aalten, D.M.F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Purification, Crystallisation and Preliminary X-Ray Difffraction of a Proteolytic Fragment of Pdk1, Containing the Pleckstrin Homology Domain
Authors: Komander, D. / Deak, M. / Morrice, N. / Van Aalten, D.M.F.
History
DepositionJun 21, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)18,6054
Polymers17,8161
Non-polymers7893
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.399, 58.922, 36.578
Angle α, β, γ (deg.)90.00, 101.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17816.186 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 409-556
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au
#4: Chemical ChemComp-4IP / INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE


Mass: 500.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16O18P4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.1 Å3/Da / Density % sol: 0.41 %
Crystal growDetails: 0.08 M MAGNESIUM ACETATE, 0.05M SODIUM CACODYLATE PH 6.5, 30 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.861,1.040
DetectorType: ADSC CCD / Detector: CCD / Date: May 5, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8611
21.041
ReflectionResolution: 1.5→25 Å / Num. obs: 23341 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.7
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RSPSphasing
MLPHAREphasing
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.332 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE CHAINS OF SOME DISORDERED RESIDUES WERE REFINED EITHER WITH THE OCCUPANCY SET TO 0.02, OR THE RESIDUE WAS MUTATED TO ALA.
RfactorNum. reflection% reflectionSelection details
Rfree0.2 617 2.7 %RANDOM
Rwork0.145 ---
obs0.147 22641 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å2-0.44 Å2
2---0.64 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 35 217 1447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211287
X-RAY DIFFRACTIONr_bond_other_d0.0020.021113
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.9651746
X-RAY DIFFRACTIONr_angle_other_deg0.95832604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7175142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1310.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021376
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02267
X-RAY DIFFRACTIONr_nbd_refined0.2170.2241
X-RAY DIFFRACTIONr_nbd_other0.2640.21308
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.2707
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2142
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6571.5721
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.38321169
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2253566
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.624.5577
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.238 43
Rwork0.206 1673

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