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- PDB-1gzo: Structure of protein kinase B unphosphorylated -

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Basic information

Entry
Database: PDB / ID: 1gzo
TitleStructure of protein kinase B unphosphorylated
ComponentsRAC-BETA SERINE/THREONINE PROTEIN KINASE
KeywordsKINASE / TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING
Function / homology
Function and homology information


retinal rod cell apoptotic process / PDE3B signalling / cellular response to high light intensity / Inhibition of TSC complex formation by PKB / AKT-mediated inactivation of FOXO1A / Negative regulation of the PI3K/AKT network / negative regulation of long-chain fatty acid import across plasma membrane / Activation of AKT2 / AKT phosphorylates targets in the nucleus / : ...retinal rod cell apoptotic process / PDE3B signalling / cellular response to high light intensity / Inhibition of TSC complex formation by PKB / AKT-mediated inactivation of FOXO1A / Negative regulation of the PI3K/AKT network / negative regulation of long-chain fatty acid import across plasma membrane / Activation of AKT2 / AKT phosphorylates targets in the nucleus / : / RUNX2 regulates genes involved in cell migration / positive regulation of fatty acid beta-oxidation / mammary gland epithelial cell differentiation / RAB GEFs exchange GTP for GDP on RABs / positive regulation of glucose metabolic process / peripheral nervous system myelin maintenance / glycogen biosynthetic process / positive regulation of cell motility / AKT phosphorylates targets in the cytosol / Regulation of TP53 Activity through Association with Co-factors / CTLA4 inhibitory signaling / fat cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / CD28 dependent PI3K/Akt signaling / Regulation of localization of FOXO transcription factors / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of glycogen biosynthetic process / Activation of BAD and translocation to mitochondria / positive regulation of protein targeting to membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / regulation of cell migration / Regulation of TP53 Activity through Acetylation / FLT3 Signaling / Downregulation of ERBB2:ERBB3 signaling / VEGFR2 mediated vascular permeability / molecular function activator activity / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / positive regulation of glucose import / TP53 Regulates Metabolic Genes / protein modification process / ruffle membrane / Regulation of PTEN stability and activity / G beta:gamma signalling through PI3Kgamma / cellular response to insulin stimulus / glucose metabolic process / KEAP1-NFE2L2 pathway / Regulation of TP53 Degradation / PIP3 activates AKT signaling / insulin receptor signaling pathway / regulation of translation / cell cortex / early endosome / non-specific serine/threonine protein kinase / regulation of cell cycle / intracellular signal transduction / positive regulation of cell migration / phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Protein Kinase B beta, catalytic domain / Protein Kinase B, pleckstrin homology domain / Protein kinase, C-terminal / Protein kinase C terminal domain / 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. ...Protein Kinase B beta, catalytic domain / Protein Kinase B, pleckstrin homology domain / Protein kinase, C-terminal / Protein kinase C terminal domain / 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 / 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
RAC-beta serine/threonine-protein kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsBarford, D. / Yang, J. / Hemmings, B.A.
CitationJournal: Mol.Cell / Year: 2002
Title: Molecular Mechanism for the Regulation of Protein Kinase B/Akt by Hydrophobic Motif Phosphorylation
Authors: Yang, J. / Cron, P. / Thompson, V. / Good, V. / Hess, D. / Hemmings, B.A. / Barford, D.
History
DepositionMay 24, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAC-BETA SERINE/THREONINE PROTEIN KINASE


Theoretical massNumber of molelcules
Total (without water)36,4911
Polymers36,4911
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)149.703, 149.703, 39.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein RAC-BETA SERINE/THREONINE PROTEIN KINASE / PROTEIN KINASE AKT-2 / PROTEIN KINASE B BETA / RAC-PK-BETA / PKB BETA


Mass: 36490.875 Da / Num. of mol.: 1
Fragment: KINASE DOMAIN WITHOUT HYDROPHOBIC MOTIF, RESIDUES 146-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P31751, 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.: 95 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: PROTEIN KINASE PHOSPHORYLATING SEVERAL KNOWN PROTEINS. TISSUE SPECIFICITY: ALL HUMAN CELL ...FUNCTION: PROTEIN KINASE PHOSPHORYLATING SEVERAL KNOWN PROTEINS. TISSUE SPECIFICITY: ALL HUMAN CELL TYPES. DISEASE: ALTERATIONS MAY CONTRIBUTE TO THE PATHOGENESIS OF OVARIAN CARCINOMAS. SIMILARITY: MEMBER OF THE SER/THR FAMILY OF PROTEIN KINASES. RAC SUBFAMILY.

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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: 2.6 Å3/Da / Density % sol: 47 %
Crystal growpH: 7.5
Details: 30% PEG 8000, 0.2 M LITHIUM SULPHATE, 0.1 M TRIS, 10MG/ML PROTEIN, pH 7.50
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein11
25 mMAMP-PNP-MgCl211
330 %(w/v)PEG40011
40.2 Mlithium sulfate11
50.1 MTris-HCl11pH8.5
65 mMdithiothreitol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 12147 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 104.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 18
Reflection shellResolution: 2.75→2.85 Å / % possible all: 84
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Num. measured all: 50875 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 84 % / Rmerge(I) obs: 0.236

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CDK

1cdk


Resolution: 2.75→25.67 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1488479.19 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1199 10.4 %RANDOM
Rwork0.248 ---
obs0.248 11519 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.6653 Å2 / ksol: 0.308053 e/Å3
Displacement parametersBiso mean: 57.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.96 Å20 Å20 Å2
2--5.96 Å20 Å2
3----11.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.75→25.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 0 95 2293
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.443 185 10.7 %
Rwork0.395 1546 -
obs--88.2 %
Refinement
*PLUS
Lowest resolution: 35 Å / % reflection Rfree: 9.9 % / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0112
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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