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- PDB-1q61: PKA triple mutant model of PKB -

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Basic information

Entry
Database: PDB / ID: 1q61
TitlePKA triple mutant model of PKB
Components
  • cAMP-dependent protein kinase inhibitor, alpha formCAMP-dependent pathway
  • cAMP-dependent protein kinase, alpha-catalytic subunitCAMP-dependent pathway
KeywordsTransferase/Transferase Inhibitor / PKB-Model / Restoration of ATP-site / point mutation / Transferase-Transferase Inhibitor COMPLEX
Function / homology
Function and homology information


CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production ...CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / PKA activation / negative regulation of cAMP-dependent protein kinase activity / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / Vasopressin regulates renal water homeostasis via Aquaporins / negative regulation of protein import into nucleus / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / protein kinase A signaling / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / protein kinase activity / protein domain specific binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
N-OCTANOYL-N-METHYLGLUCAMINE / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGassel, M. / Breitenlechner, C.B. / Rueger, P. / Jucknischke, U. / Schneider, T. / Huber, R. / Bossemeyer, D. / Engh, R.A.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Mutants of protein kinase A that mimic the ATP-binding site of protein kinase B (AKT)
Authors: Gassel, M. / Breitenlechner, C.B. / Rueger, P. / Jucknischke, U. / Schneider, T. / Huber, R. / Bossemeyer, D. / Engh, R.A.
#1: Journal: Embo J. / Year: 1993
Title: Phosphotransferase and substrate binding mechanism of the cAMP-dependent protein kinase catalytic subunit from porcine heart as deduced from the 2.0 A structure of the complex with Mn2+ ...Title: Phosphotransferase and substrate binding mechanism of the cAMP-dependent protein kinase catalytic subunit from porcine heart as deduced from the 2.0 A structure of the complex with Mn2+ adenylyl imidodiphosphate and inhibitor peptide PKI(5-24)
Authors: Bossemeyer, D. / Engh, R.A. / Kinzel, V. / Ponstingl, H. / Huber, R.
History
DepositionAug 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cAMP-dependent protein kinase, alpha-catalytic subunit
I: cAMP-dependent protein kinase inhibitor, alpha form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2453
Polymers42,9242
Non-polymers3211
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint3 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.870, 79.420, 100.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cAMP-dependent protein kinase, alpha-catalytic subunit / CAMP-dependent pathway / PKA C-alpha


Mass: 40697.449 Da / Num. of mol.: 1 / Mutation: V123A, L173M, Q181K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKACA / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00517, EC: 2.7.1.37
#2: Protein/peptide cAMP-dependent protein kinase inhibitor, alpha form / CAMP-dependent pathway / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: residues 5-24 / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN Homo Sapiens.
References: UniProt: P04541, UniProt: P61925*PLUS
#3: Chemical ChemComp-MG8 / N-OCTANOYL-N-METHYLGLUCAMINE / MEGA 8 / N-(D-GLUCITYL)-N-METHYLOCTANAMIDE


Mass: 321.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H31NO6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: MES-Bistris, LiCl, DTT, Mega8, PKI, methanol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: BRUKER / Detector: AREA DETECTOR / Date: Jul 19, 2001
RadiationMonochromator: Graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→7.97 Å / Num. obs: 26309 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.14

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SAINTdata reduction
SAINTdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→7.97 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.091 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23234 2642 10 %RANDOM
Rwork0.17859 ---
obs0.18403 23666 93.43 %-
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: 27.656 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→7.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 8 154 3103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212953
X-RAY DIFFRACTIONr_bond_other_d0.0060.022645
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9423995
X-RAY DIFFRACTIONr_angle_other_deg0.92636118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0465355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023279
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02648
X-RAY DIFFRACTIONr_nbd_refined0.2120.2523
X-RAY DIFFRACTIONr_nbd_other0.2380.22907
X-RAY DIFFRACTIONr_nbtor_other0.0910.21719
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2122
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8591.51777
X-RAY DIFFRACTIONr_mcangle_it1.59522852
X-RAY DIFFRACTIONr_scbond_it2.33731176
X-RAY DIFFRACTIONr_scangle_it3.8094.51143
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.151 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.327 152
Rwork0.241 1645

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