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- PDB-1w1g: Crystal Structure of the PDK1 Pleckstrin Homology (PH) domain bou... -

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Basic information

Entry
Database: PDB / ID: 1w1g
TitleCrystal Structure of the PDK1 Pleckstrin Homology (PH) domain bound to DiC4-phosphatidylinositol (3,4,5)-trisphosphate
Components3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1
KeywordsTRANSFERASE / PDK1 / PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1 / PKB / PLECKSTRIN HOMOLOGY DOMAIN / INOSITOL PHOSPHATE / PHOSPHOINOSITIDE / SIGNAL TRANSDUCTION / PI3-KINASE / PIP3 SERINE/THREONINE PROTEIN KINASE
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 / 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 ...PDK1-type, PH domain / PDPK1 family / PH domain / 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
Chem-4PT / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKomander, D. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
CitationJournal: 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.
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 ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
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)18,5332
Polymers17,8161
Non-polymers7161
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.264, 58.943, 36.440
Angle α, β, γ (deg.)90.00, 102.33, 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-4PT / (2R)-3-{[(S)-{[(2S,3R,5S,6S)-2,6-DIHYDROXY-3,4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-(1-HYDROXY BUTOXY)PROPYL BUTYRATE / DIC4-PHOSPHATIDYLINOSITOL(3,4,5)TRISPHOSPHATE


Mass: 716.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O22P4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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 growpH: 4.2
Details: 25 % PEG 4000, 0.1 M SODIUM ACETATE [PH 4.2], 0.3 M AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS 4 / Detector: IMAGE PLATE / Date: Sep 15, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 25810 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.8
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDK1PH INSP4 MODEL

Resolution: 1.45→25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.471 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.081 / 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. THE ACYL- ...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. THE ACYL-CHAINS OF THE LIGAND WERE NOT MODELLED DUE TO DISORDER.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 545 2.1 %RANDOM
Rwork0.182 ---
obs0.183 25241 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.94 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20.06 Å2
2---0.83 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.45→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 33 163 1390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221273
X-RAY DIFFRACTIONr_bond_other_d0.0020.021115
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9611731
X-RAY DIFFRACTIONr_angle_other_deg0.863.0012588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6225142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69323.73167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7115219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7081510
X-RAY DIFFRACTIONr_chiral_restr0.1090.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021363
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02263
X-RAY DIFFRACTIONr_nbd_refined0.2210.2267
X-RAY DIFFRACTIONr_nbd_other0.20.21116
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2613
X-RAY DIFFRACTIONr_nbtor_other0.1070.2672
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2740.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7271.5746
X-RAY DIFFRACTIONr_mcbond_other0.7451.5287
X-RAY DIFFRACTIONr_mcangle_it2.30521168
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6143612
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9234.5563
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: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 44 -
Rwork0.339 1834 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.16790.1263-0.14291.4071-0.56040.4956-0.0012-0.01410.0265-0.07630.0301-0.00920.0443-0.0069-0.0288-0.0377-0.0001-0.00040.0133-0.0049-0.008810.538827.174624.0723
20.47420.2713-0.21951.4621-0.8330.48450.02780.02030.0334-0.09060.06710.07770.04980.0051-0.095-0.0232-0.0101-0.0146-0.0096-0.0199-0.03049.568426.773922.819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A414 - 466
2X-RAY DIFFRACTION1A472 - 487
3X-RAY DIFFRACTION1A494 - 543
4X-RAY DIFFRACTION2A408 - 413
5X-RAY DIFFRACTION2A466 - 471
6X-RAY DIFFRACTION2A544 - 549
7X-RAY DIFFRACTION2A488 - 493

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