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- PDB-6yqi: Crystal structure of cAMP-dependent Protein Kinase (PKA) in compl... -

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Basic information

Entry
Database: PDB / ID: 6yqi
TitleCrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with long-chain Fasudil-derivative N-[2-(propylamino)ethyl]isoquinoline-5-sulfonamide (soaked)
Components
  • cAMP-dependent protein kinase catalytic subunit alpha
  • cAMP-dependent protein kinase inhibitor alpha
KeywordsTRANSFERASE / phosphotransferase / signalling pathways / glycogen metabolism / serine/threonine kinase
Function / homology
Function and homology information


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 ...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 / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / mesoderm formation / plasma membrane raft / axoneme / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / regulation of G2/M transition of mitotic cell cycle / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / acrosomal vesicle / protein export from nucleus / positive regulation of phagocytosis / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / neuromuscular junction / cellular response to glucose stimulus / positive regulation of cholesterol biosynthetic process / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / adenylate cyclase-activating G protein-coupled receptor signaling pathway / manganese ion binding / cellular response to heat / postsynapse / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / centrosome / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol
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. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...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. / 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
Similarity search - Domain/homology
Chem-6TV / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsOebbeke, M. / Wienen-Schmidt, B. / Heine, A. / Klebe, G.
CitationJournal: Chemmedchem / Year: 2021
Title: Two Methods, One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses.
Authors: Wienen-Schmidt, B. / Oebbeke, M. / Ngo, K. / Heine, A. / Klebe, G.
History
DepositionApr 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.3Jan 24, 2024Group: 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
B: cAMP-dependent protein kinase inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4803
Polymers43,1872
Non-polymers2931
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-1 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.107, 72.482, 108.739
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 41193.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide cAMP-dependent protein kinase inhibitor alpha / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 1993.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P63248
#3: Chemical ChemComp-6TV / ~{N}-[2-(propylamino)ethyl]isoquinoline-5-sulfonamide


Mass: 293.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.24mM PKA, 30mM MBT (MES/Bis-Tris Buffer pH 6.2-6.9), 1mM DTT, 0.1mM EDTA, 75mM LiCl, 0.3mM Mega 8, 0.7mM PKI, 16%(v/v) methanol; soaking in buffer described with 0.12mM ligand solved in DMSO and 30%(v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.417→45.337 Å / Num. obs: 86529 / % possible obs: 98.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 18.15 Å2 / Rsym value: 0.038 / Net I/σ(I): 22.72
Reflection shellResolution: 1.42→1.5 Å / Mean I/σ(I) obs: 3.12 / Num. unique obs: 13515 / Rsym value: 0.462

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q8W

1q8w


Resolution: 1.42→36.24 Å / SU ML: 0.1017 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.2605
RfactorNum. reflection% reflection
Rfree0.1801 4326 5 %
Rwork0.1537 --
obs0.155 86523 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.6 Å2
Refinement stepCycle: LAST / Resolution: 1.42→36.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 0 20 296 3148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672976
X-RAY DIFFRACTIONf_angle_d0.92924046
X-RAY DIFFRACTIONf_chiral_restr0.071433
X-RAY DIFFRACTIONf_plane_restr0.0066532
X-RAY DIFFRACTIONf_dihedral_angle_d20.09391072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.430.24071320.18732506X-RAY DIFFRACTION91.47
1.43-1.450.23931410.17652684X-RAY DIFFRACTION97.25
1.45-1.470.20791400.16432654X-RAY DIFFRACTION98.07
1.47-1.490.22641420.15352705X-RAY DIFFRACTION97.84
1.49-1.510.18511420.14592687X-RAY DIFFRACTION97.79
1.51-1.530.18931410.14112681X-RAY DIFFRACTION98.26
1.53-1.550.1661430.13042728X-RAY DIFFRACTION97.95
1.55-1.570.16671430.12812703X-RAY DIFFRACTION98.1
1.57-1.60.14611400.12372669X-RAY DIFFRACTION98.46
1.6-1.620.18061440.11652729X-RAY DIFFRACTION98.42
1.62-1.650.13511420.1212691X-RAY DIFFRACTION97.96
1.65-1.680.15711430.11942731X-RAY DIFFRACTION98.66
1.68-1.710.15911450.11392751X-RAY DIFFRACTION98.97
1.71-1.750.15881430.11692710X-RAY DIFFRACTION98.72
1.75-1.790.15731430.11662731X-RAY DIFFRACTION98.63
1.79-1.830.15281430.12622713X-RAY DIFFRACTION98.69
1.83-1.870.15071450.13242760X-RAY DIFFRACTION98.91
1.87-1.920.17791450.13332737X-RAY DIFFRACTION99.04
1.92-1.980.16311430.13852734X-RAY DIFFRACTION99.04
1.98-2.040.15611450.14322751X-RAY DIFFRACTION99.08
2.04-2.120.16551450.14932754X-RAY DIFFRACTION99.25
2.12-2.20.18121450.14422761X-RAY DIFFRACTION98.98
2.2-2.30.16281470.14012778X-RAY DIFFRACTION99.63
2.3-2.420.14781470.14052800X-RAY DIFFRACTION99.46
2.42-2.570.18241460.14412769X-RAY DIFFRACTION99.76
2.57-2.770.18181470.16272795X-RAY DIFFRACTION99.46
2.77-3.050.1951480.16892811X-RAY DIFFRACTION99.43
3.05-3.490.19211480.17062821X-RAY DIFFRACTION99.53
3.49-4.40.16291500.16012853X-RAY DIFFRACTION99.11
4.4-36.240.22991580.1843000X-RAY DIFFRACTION99.59

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