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- PDB-1q24: PKA double mutant model of PKB in complex with MgATP -

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Basic information

Entry
Database: PDB / ID: 1q24
TitlePKA double mutant model of PKB in complex with MgATP
Components
  • cAMP-dependent Protein Kinase Inhibitor, alpha form
  • cAMP-dependent Protein Kinase, alpha-catalytic subunit
KeywordsTRANSFERASE/TRANSFERASE inhibitor / Q181 switch / Mg-ATP binding / PKB-model / 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 / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / negative regulation of protein import into nucleus / Vasopressin regulates renal water homeostasis via Aquaporins / Mitochondrial protein degradation / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / protein kinase A signaling / 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
ADENOSINE-5'-TRIPHOSPHATE / 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: 2.6 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
DepositionJul 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 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
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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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)43,4544
Polymers42,9232
Non-polymers5312
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-17 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.286, 75.387, 80.377
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 / PKA C-alpha


Mass: 40696.398 Da / Num. of mol.: 1 / Mutation: V123A, L173M
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 (bacteria) / Strain (production host): BL21 / References: UniProt: P00517, EC: 2.7.1.37
#2: Protein/peptide cAMP-dependent Protein Kinase Inhibitor, alpha form / PKI-alpha


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: Q71U53*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 277.16 K / pH: 6.4
Details: Mes-Bistris, LiCl, DTT, Mega8, PKI, ATP, MgCl, , pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.16K, pH 6.40
Crystal grow
*PLUS
Temperature: 5 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.6 / PH range high: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
118 mg/mlprotein1drop
225 mMMES-Bis Tris1drop
375 mM1dropLiCl
40.1 mM1dropMgCl2
51 mMdithiothreitol1drop
61.5 mMoctanoyl-N-methylglucamide1drop
71 mMPKI-(5-24)1droppH6.3-6.6
81.5 mMATP1drop
93 mM1dropMgCl2
1012-18 %(v/v)methanol1reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: BRUKER / Detector: AREA DETECTOR / Date: Feb 4, 2002 / Details: 0.3 MM COLLIMATOR
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→8.05 Å / Num. obs: 11741 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.097
Reflection
*PLUS
Highest resolution: 2.6 Å / % possible obs: 86 % / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 72 % / Rmerge(I) obs: 0.39

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SAINTdata reduction
SAINTdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→8.05 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.883 / SU B: 12.575 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1207 10.3 %RANDOM
Rwork0.196 ---
obs0.202 10534 85.8 %-
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: 19.01 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→8.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2941 0 32 132 3105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212972
X-RAY DIFFRACTIONr_bond_other_d0.0020.022605
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.9524034
X-RAY DIFFRACTIONr_angle_other_deg0.78236038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995355
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_restr0.0690.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023296
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02640
X-RAY DIFFRACTIONr_nbd_refined0.1890.2627
X-RAY DIFFRACTIONr_nbd_other0.2140.23100
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.21749
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2108
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4181.51774
X-RAY DIFFRACTIONr_mcangle_it0.79422846
X-RAY DIFFRACTIONr_scbond_it1.03631198
X-RAY DIFFRACTIONr_scangle_it1.8194.51188
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.66 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.422 67
Rwork0.267 617
Refinement
*PLUS
Highest resolution: 2.6 Å / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.191 / Rfactor Rwork: 0.161

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