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- PDB-1unp: Crystal structure of the pleckstrin homology domain of PKB alpha -

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Basic information

Entry
Database: PDB / ID: 1unp
TitleCrystal structure of the pleckstrin homology domain of PKB alpha
ComponentsRAC-ALPHA SERINE/THREONINE KINASE
KeywordsTRANSFERASE / PLECKSTRIN HOMOLOGY DOMAIN / PHOSPHOINOSITIDE / PKB / AKT
Function / homology
Function and homology information


glycogen cell differentiation involved in embryonic placenta development / regulation of tRNA methylation / response to insulin-like growth factor stimulus / mammalian oogenesis stage / potassium channel activator activity / negative regulation of protein localization to lysosome / positive regulation of protein localization to endoplasmic reticulum / maintenance of protein location in mitochondrion / negative regulation of lymphocyte migration / cellular response to decreased oxygen levels ...glycogen cell differentiation involved in embryonic placenta development / regulation of tRNA methylation / response to insulin-like growth factor stimulus / mammalian oogenesis stage / potassium channel activator activity / negative regulation of protein localization to lysosome / positive regulation of protein localization to endoplasmic reticulum / maintenance of protein location in mitochondrion / negative regulation of lymphocyte migration / cellular response to decreased oxygen levels / maternal placenta development / regulation of type B pancreatic cell development / AKT-mediated inactivation of FOXO1A / Negative regulation of the PI3K/AKT network / negative regulation of long-chain fatty acid import across plasma membrane / establishment of protein localization to mitochondrion / activation-induced cell death of T cells / negative regulation of fatty acid beta-oxidation / regulation of glycogen biosynthetic process / AKT phosphorylates targets in the nucleus / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of I-kappaB phosphorylation / negative regulation of cilium assembly / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / response to fluid shear stress / RUNX2 regulates genes involved in cell migration / positive regulation of organ growth / interleukin-18-mediated signaling pathway / MTOR signalling / fibroblast migration / positive regulation of sodium ion transport / mammary gland epithelial cell differentiation / negative regulation of endopeptidase activity / negative regulation of protein serine/threonine kinase activity / positive regulation of protein localization to cell surface / RAB GEFs exchange GTP for GDP on RABs / positive regulation of endodeoxyribonuclease activity / protein serine/threonine kinase inhibitor activity / positive regulation of glucose metabolic process / response to growth factor / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of leukocyte cell-cell adhesion / phosphatidylinositol-3,4-bisphosphate binding / peripheral nervous system myelin maintenance / sphingosine-1-phosphate receptor signaling pathway / glycogen biosynthetic process / positive regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / response to growth hormone / anoikis / regulation of postsynapse organization / AKT phosphorylates targets in the cytosol / execution phase of apoptosis / labyrinthine layer blood vessel development / response to food / regulation of myelination / response to UV-A / KSRP (KHSRP) binds and destabilizes mRNA / Regulation of TP53 Activity through Association with Co-factors / negative regulation of macroautophagy / CTLA4 inhibitory signaling / negative regulation of cGAS/STING signaling pathway / behavioral response to pain / regulation of neuron projection development / negative regulation of Notch signaling pathway / TOR signaling / negative regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / Constitutive Signaling by AKT1 E17K in Cancer / non-canonical NF-kappaB signal transduction / phosphatidylinositol-3,4,5-trisphosphate binding / CD28 dependent PI3K/Akt signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / Regulation of localization of FOXO transcription factors / carbohydrate transport / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of BAD and translocation to mitochondria / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of fat cell differentiation / positive regulation of blood vessel endothelial cell migration / positive regulation of glycogen biosynthetic process / cellular response to vascular endothelial growth factor stimulus / positive regulation of lipid biosynthetic process / canonical NF-kappaB signal transduction / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / eNOS activation / Cyclin E associated events during G1/S transition / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of cell migration / Cyclin A:Cdk2-associated events at S phase entry / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / negative regulation of protein ubiquitination / lipopolysaccharide-mediated signaling pathway / cellular response to epidermal growth factor stimulus / cellular response to cadmium ion / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TP53 Activity through Acetylation / positive regulation of TORC1 signaling / regulation of mRNA stability
Similarity search - Function
Protein kinase B alpha, catalytic domain / Protein Kinase B, pleckstrin homology domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain ...Protein kinase B alpha, catalytic domain / Protein Kinase B, pleckstrin homology domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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
RAC-alpha serine/threonine-protein kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsMilburn, C.C. / Deak, M. / Kelly, S.M. / Price, N.C. / Alessi, D.R. / van Aalten, D.M.F.
Citation
Journal: Biochem. J. / Year: 2003
Title: Binding of phosphatidylinositol 3,4,5-trisphosphate to the pleckstrin homology domain of protein kinase B induces a conformational change.
Authors: Milburn, C.C. / Deak, M. / Kelly, S.M. / Price, N.C. / Alessi, D.R. / Van Aalten, D.M.
#1: Journal: Curr.Biol. / Year: 2002
Title: High-Resolution Structure of the Pleckstrin Homology Domain of Protein Kinase B/Akt Bound to Phosphatidylinositol (3,4,5)-Trisphosphate
Authors: Thomas, C.C. / Deak, M. / Alessi, D.R. / Van Aalten, M.F.
History
DepositionSep 12, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAC-ALPHA SERINE/THREONINE KINASE


Theoretical massNumber of molelcules
Total (without water)14,5421
Polymers14,5421
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.064, 33.803, 42.071
Angle α, β, γ (deg.)90.00, 119.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RAC-ALPHA SERINE/THREONINE KINASE / RAC-PK-ALPHA / PROTEIN KINASE B / PKB / C-AKT


Mass: 14542.459 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 1-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX4T-1 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P31749, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 1.75 Å3/Da / Density % sol: 30 %
Crystal growpH: 8.5
Details: 30 % PEG 4000, 0.25 M SODIUM ACETATE, 0.1 M TRIS PH 8.5 3.3 % POLYPROPYLENE GLYCOL 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97949
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 12409 / % possible obs: 98.7 % / Redundancy: 3 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 4.1
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 4.1 / % possible all: 97.2

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1H10

1h10


Resolution: 1.65→19.78 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 873989.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 601 4.8 %RANDOM
Rwork0.201 ---
obs0.201 12394 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.3137 Å2 / ksol: 0.42143 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.37 Å20 Å2-1.61 Å2
2--6.4 Å20 Å2
3----4.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.65→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 0 0 132 1141
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.591.5
X-RAY DIFFRACTIONc_mcangle_it2.592
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.172.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 90 4.4 %
Rwork0.269 1941 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMPROTEIN_BREAK.TOP
X-RAY DIFFRACTION3PROTEIN.LINK
X-RAY DIFFRACTION4WATER.TOP

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