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- PDB-9re1: Crystal Structure of the Protein-Kinase A catalytic subunit from ... -

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Basic information

Entry
Database: PDB / ID: 9re1
TitleCrystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus griseus in complex with F055
ComponentscAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / serine-threonine kinase / small molecules / ligand binding / fragment-based drug discovery
Function / homology
Function and homology information


cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / 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 / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / 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 / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / positive regulation of gluconeogenesis / 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 / positive regulation of insulin secretion / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / 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 / cytosol / cytoplasm
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
: / DI(HYDROXYETHYL)ETHER / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsMetz, A. / Mueller, J.M. / Wolter, M. / Glinca, S. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Chem.Inf.Model. / Year: 2025
Title: Natural Product-like Fragments Unlock Novel Chemotypes for a Kinase Target Exploring Options beyond the Flatland
Authors: Santura, A. / Muller, J. / Wolter, M. / Tutzschky, I.C. / Ruf, M. / Metz, A. / Sandner, A. / Merkl, S. / Klebe, G. / Glinca, S. / Czodrowski, P.
History
DepositionJun 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release

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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)42,0758
Polymers41,1141
Non-polymers9617
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint7 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.826, 71.964, 98.391
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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P25321, cAMP-dependent protein kinase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-A1JE2 / 1-[4-[(1~{S},2~{S},3~{S},4~{R},5~{R})-2-azanyl-3-oxidanyl-6,8-dioxabicyclo[3.2.1]octan-4-yl]piperazin-1-yl]ethanone


Mass: 271.313 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H21N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Mes/Bis-Tris, 75 mM lithium chloride, 1 mM DTT, 0.1 mM sodium EDTA, 0.25 mM Mega 8, 23% v/v methanol/water in reservoir

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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: Jan 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.41→45.85 Å / Num. obs: 71614 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Net I/σ(I): 18.4
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3496 / CC1/2: 0.636 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→45.85 Å / SU ML: 0.1592 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.5304
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1892 3659 5.11 %
Rwork0.1561 67877 -
obs0.1578 71536 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.59 Å2
Refinement stepCycle: LAST / Resolution: 1.41→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 61 327 3157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093212
X-RAY DIFFRACTIONf_angle_d1.00074390
X-RAY DIFFRACTIONf_chiral_restr0.0912464
X-RAY DIFFRACTIONf_plane_restr0.0094569
X-RAY DIFFRACTIONf_dihedral_angle_d15.55931198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.430.33891330.26282564X-RAY DIFFRACTION99.85
1.43-1.450.30711430.23532571X-RAY DIFFRACTION99.89
1.45-1.470.24261210.20252621X-RAY DIFFRACTION99.85
1.47-1.490.23571260.18152572X-RAY DIFFRACTION99.74
1.49-1.510.22181400.17762558X-RAY DIFFRACTION99.89
1.51-1.540.21241540.17522589X-RAY DIFFRACTION100
1.54-1.570.25321410.17712580X-RAY DIFFRACTION99.78
1.57-1.590.25511260.18462593X-RAY DIFFRACTION100
1.59-1.620.21311320.18342588X-RAY DIFFRACTION99.96
1.62-1.660.20831490.16922573X-RAY DIFFRACTION99.96
1.66-1.690.20871220.15392612X-RAY DIFFRACTION99.89
1.69-1.730.22451470.1442597X-RAY DIFFRACTION99.89
1.73-1.780.1841410.13812580X-RAY DIFFRACTION99.96
1.78-1.820.16091390.13592602X-RAY DIFFRACTION99.96
1.82-1.880.18531350.14472596X-RAY DIFFRACTION99.67
1.88-1.940.19241600.15262586X-RAY DIFFRACTION100
1.94-2.010.23451390.16122615X-RAY DIFFRACTION100
2.01-2.090.17581380.14712604X-RAY DIFFRACTION99.96
2.09-2.180.17841510.14452622X-RAY DIFFRACTION99.89
2.18-2.30.20461580.14292577X-RAY DIFFRACTION99.74
2.3-2.440.19731300.14872628X-RAY DIFFRACTION99.78
2.44-2.630.15931370.15542653X-RAY DIFFRACTION100
2.63-2.90.1821340.16332667X-RAY DIFFRACTION100
2.9-3.310.20441510.16282643X-RAY DIFFRACTION99.68
3.32-4.180.15911380.1462693X-RAY DIFFRACTION99.72
4.18-45.850.17141740.15422793X-RAY DIFFRACTION99.43

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