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- PDB-9re3: Crystal Structure of the Protein-Kinase A catalytic subunit from ... -

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Basic information

Entry
Database: PDB / ID: 9re3
TitleCrystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus griseus in complex with F070
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
: / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsRuf, M. / 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)41,9958
Polymers41,1141
Non-polymers8817
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint9 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.398, 72.624, 98.995
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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-A1JE0 / 2-(4-methoxyphenyl)-5-[(3~{S})-pyrrolidin-3-yl]-1,3,4-oxadiazole


Mass: 245.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
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: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.57→46.31 Å / Num. obs: 52571 / % possible obs: 98.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 21.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.7
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 6 % / Rmerge(I) obs: 1.179 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2558 / CC1/2: 0.669 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→29.28 Å / SU ML: 0.226 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6646
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2127 2604 4.96 %
Rwork0.1833 49889 -
obs0.1848 52493 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.38 Å2
Refinement stepCycle: LAST / Resolution: 1.57→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 56 242 3023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02073039
X-RAY DIFFRACTIONf_angle_d1.34734155
X-RAY DIFFRACTIONf_chiral_restr0.1014442
X-RAY DIFFRACTIONf_plane_restr0.0124534
X-RAY DIFFRACTIONf_dihedral_angle_d12.83451096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.60.41891200.45692622X-RAY DIFFRACTION98
1.6-1.630.42431270.38982565X-RAY DIFFRACTION98.18
1.63-1.660.35061540.29852569X-RAY DIFFRACTION98.16
1.66-1.70.2991540.25642586X-RAY DIFFRACTION98.17
1.7-1.740.25041450.21612576X-RAY DIFFRACTION98.27
1.74-1.780.21991120.20012432X-RAY DIFFRACTION91.68
1.78-1.830.24511280.20552565X-RAY DIFFRACTION96.28
1.83-1.880.29711340.22022611X-RAY DIFFRACTION98.92
1.88-1.940.25391320.20092655X-RAY DIFFRACTION99.01
1.94-2.010.20981390.16412621X-RAY DIFFRACTION98.68
2.01-2.090.21261280.16632633X-RAY DIFFRACTION99.17
2.09-2.190.2021420.16572654X-RAY DIFFRACTION99.4
2.19-2.310.19521400.16642640X-RAY DIFFRACTION99.18
2.31-2.450.24011340.17072652X-RAY DIFFRACTION99.32
2.45-2.640.22751510.17872663X-RAY DIFFRACTION99.58
2.64-2.90.19141510.18722686X-RAY DIFFRACTION99.23
2.9-3.320.19661460.17912553X-RAY DIFFRACTION94.44
3.32-4.180.16121310.15862728X-RAY DIFFRACTION99.31
4.19-29.280.19071360.16742878X-RAY DIFFRACTION99.47

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