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- PDB-2gfc: cAMP-dependent protein kinase PKA catalytic subunit with PKI-5-24 -

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Basic information

Entry
Database: PDB / ID: 2gfc
TitlecAMP-dependent protein kinase PKA catalytic subunit with PKI-5-24
Components
  • cAMP-dependent protein kinase inhibitor alpha
  • cAMP-dependent protein kinase, alpha-catalytic subunit
KeywordsTRANSFERASE / binary complex / peptide inhibitor
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 / negative regulation of cAMP-dependent protein kinase activity / VEGFA-VEGFR2 Pathway / PKA activation / Hedgehog 'off' state / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / Regulation of PLK1 Activity at G2/M Transition / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus / molecular function inhibitor activity / cellular response to cold / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / regulation of osteoblast differentiation / sperm capacitation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / negative regulation of glycolytic process through fructose-6-phosphate / Mitochondrial protein degradation / ciliary base / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / plasma membrane raft / axoneme / postsynaptic modulation of chemical synaptic transmission / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / cellular response to glucagon stimulus / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / manganese ion binding / cellular response to heat / peptidyl-serine phosphorylation / molecular adaptor activity / regulation of cell cycle / protein kinase activity / postsynapse / nuclear speck / protein phosphorylation / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / mitochondrion / ATP binding / nucleus / 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. / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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. / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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-OCTANE / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsBonn, S. / Herrero, S. / Breitenlechner, C.B. / Engh, R.A. / Gassel, M. / Bossemeyer, D.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural Analysis of Protein Kinase A Mutants with Rho-kinase Inhibitor Specificity.
Authors: Bonn, S. / Herrero, S. / Breitenlechner, C.B. / Erlbruch, A. / Lehmann, W. / Engh, R.A. / Gassel, M. / Bossemeyer, D.
History
DepositionMar 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
A: N-OCTANE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0473
Polymers42,9332
Non-polymers1141
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint3 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.492, 75.533, 80.387
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: 40706.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: PRKACA / Plasmid: PT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P00517, EC: 2.7.1.37
#2: Protein/peptide cAMP-dependent protein kinase inhibitor alpha / PKI-alpha / cAMP- dependent protein kinase inhibitor / muscle/brain isoform


Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: Inhibitory Fragment (Residues: 5 to 24) / Source method: obtained synthetically / Details: Peptide Synthesis / References: UniProt: P61926
#3: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15 % Methanol, 75 mM LiCl, 30 mM MesBisTris, 1 mM DTT, 0.2 mM EDTA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.00076 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00076 Å / Relative weight: 1
ReflectionResolution: 1.642→55.048 Å / Num. all: 54383 / Num. obs: 54188 / % possible obs: 99.77 % / Observed criterion σ(F): 514.1 / Observed criterion σ(I): 4.9

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Processing

SoftwareName: REFMAC / Version: 5.1.24 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AN UNPUBLISHED STRUCTURE OF THE BINARY COMPLEX OF BOVINE PKA C ALPHA ENZYME WITH PKI(5-24)

Resolution: 1.87→55.05 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.106 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.139 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23908 1888 5.1 %RANDOM
Rwork0.19196 ---
all0.23908 54326 --
obs0.19435 35182 99.77 %-
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: 25.139 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0.43 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.87→55.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 8 282 3233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223025
X-RAY DIFFRACTIONr_bond_other_d0.0020.022716
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9494078
X-RAY DIFFRACTIONr_angle_other_deg0.936331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925355
X-RAY DIFFRACTIONr_chiral_restr0.120.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023316
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02652
X-RAY DIFFRACTIONr_nbd_refined0.2080.2581
X-RAY DIFFRACTIONr_nbd_other0.2430.23089
X-RAY DIFFRACTIONr_nbtor_other0.0870.21686
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2174
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4780.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3910.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.224
X-RAY DIFFRACTIONr_mcbond_it0.9521.51777
X-RAY DIFFRACTIONr_mcangle_it1.75422866
X-RAY DIFFRACTIONr_scbond_it2.75831248
X-RAY DIFFRACTIONr_scangle_it4.4164.51212
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 137
Rwork0.264 2568

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