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- PDB-6spm: Crystal structure of cAMP-dependent protein kinase A (CHO PKA) in... -

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Basic information

Entry
Database: PDB / ID: 6spm
TitleCrystal structure of cAMP-dependent protein kinase A (CHO PKA) in complex with 4-(trifluoromethyl)benzoic acid
ComponentscAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / phosphotransferase / signalling pathways / glycogen metabolism / serine/threonine kinase
Function / homology
Function and homology information


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 / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation ...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 / 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 / intracellular potassium ion homeostasis / mesoderm formation / plasma membrane raft / axoneme / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / 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 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / 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 / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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. ...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
4-(trifluoromethyl)benzoic acid / METHANOL / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsOebbeke, M. / Siefker, C. / Heine, A. / Klebe, G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Fragment Binding to Kinase Hinge: If Charge Distribution and Local pK a Shifts Mislead Popular Bioisosterism Concepts.
Authors: Oebbeke, M. / Siefker, C. / Wagner, B. / Heine, A. / Klebe, G.
History
DepositionSep 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
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 1.4Nov 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,4925
Polymers41,1141
Non-polymers3784
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint3 kcal/mol
Surface area15200 Å2
Unit cell
Length a, b, c (Å)51.556, 71.403, 97.810
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: 41113.766 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: Chemical ChemComp-3AE / 4-(trifluoromethyl)benzoic acid


Mass: 190.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5F3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.03 Mega 8 and 23 % methanol (v/v)0.003 mL drop volume, 0.5 mL reservoir volume

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.369→45.61 Å / Num. obs: 76337 / % possible obs: 99.5 % / Redundancy: 4.4 % / Rsym value: 0.048 / Net I/σ(I): 16.78
Reflection shellResolution: 1.369→1.376 Å / Mean I/σ(I) obs: 2.71 / Num. unique obs: 12112 / Rsym value: 0.485

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Processing

Software
NameVersionClassification
PHASERphasing
Coot0.8.9model building
PHENIXrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F14

6f14


Resolution: 1.37→38.44 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36
RfactorNum. reflection% reflection
Rfree0.1695 3817 5 %
Rwork0.1463 --
obs0.1475 76332 99.5 %
Displacement parametersBiso mean: 16.83 Å2
Refinement stepCycle: LAST / Resolution: 1.37→38.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 23 306 3051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722963
X-RAY DIFFRACTIONf_angle_d0.94744039
X-RAY DIFFRACTIONf_chiral_restr0.0779428
X-RAY DIFFRACTIONf_plane_restr0.007530
X-RAY DIFFRACTIONf_dihedral_angle_d22.00711086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.24861330.19492538X-RAY DIFFRACTION95.98
1.39-1.40.21771410.17522672X-RAY DIFFRACTION99.82
1.4-1.420.20791410.16822680X-RAY DIFFRACTION99.96
1.42-1.440.1791400.16482668X-RAY DIFFRACTION99.79
1.44-1.470.19721400.15672643X-RAY DIFFRACTION99.93
1.47-1.490.18261400.1462667X-RAY DIFFRACTION99.89
1.49-1.510.1791410.14232675X-RAY DIFFRACTION99.89
1.51-1.540.16611380.1372629X-RAY DIFFRACTION99.82
1.54-1.570.18111420.13122689X-RAY DIFFRACTION99.61
1.57-1.60.17461400.12782660X-RAY DIFFRACTION99.75
1.6-1.630.15921410.12612683X-RAY DIFFRACTION99.82
1.63-1.670.16641410.1312678X-RAY DIFFRACTION99.89
1.67-1.70.17561390.13012638X-RAY DIFFRACTION99.07
1.7-1.750.1691410.12822683X-RAY DIFFRACTION99.65
1.75-1.790.16771410.12782680X-RAY DIFFRACTION99.96
1.79-1.850.17041410.12962687X-RAY DIFFRACTION99.79
1.85-1.910.14841410.13332679X-RAY DIFFRACTION99.93
1.91-1.970.17941410.13882682X-RAY DIFFRACTION99.89
1.97-2.050.15541430.12972715X-RAY DIFFRACTION99.97
2.05-2.150.15051420.13282688X-RAY DIFFRACTION99.79
2.15-2.260.16081400.13162666X-RAY DIFFRACTION98.84
2.26-2.40.16131420.13552688X-RAY DIFFRACTION98.74
2.4-2.590.16571430.1432733X-RAY DIFFRACTION99.83
2.59-2.850.16381440.15092730X-RAY DIFFRACTION99.79
2.85-3.260.16691450.15392744X-RAY DIFFRACTION99.79
3.26-4.110.16541440.14592751X-RAY DIFFRACTION99.31
4.11-38.440.181520.182869X-RAY DIFFRACTION98.15

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