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- PDB-7axt: Crystal structure of the cAMP-dependent protein kinase A cocrysta... -

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Basic information

Entry
Database: PDB / ID: 7axt
TitleCrystal structure of the cAMP-dependent protein kinase A cocrystallized with isoquinoline-5-carboxylic acid and PKI (5-24)
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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
isoquinoline-5-carboxylic acid / 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: 1.86 Å
AuthorsOebbeke, M. / Wienen-Schmidt, B. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Fragment based drug design - Small chemical changes of fragments effecting big changes in binding
Authors: Oebbeke, M. / Wienen-Schmidt, B. / Gerber, H.-D. / Heine, A. / Klebe, G.
History
DepositionNov 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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)43,5133
Polymers43,3402
Non-polymers1731
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-2 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.448, 73.258, 109.473
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: 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 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P63248
#3: Chemical ChemComp-S9B / isoquinoline-5-carboxylic acid


Mass: 173.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.86 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 30mM MBT, 1mM DTT, 0.1mM EDTA, 75mM LiCl, 0.3mM Mega8, 0.07mM PKI, 10mM of isoquinoline-5-carboxylic acid (solved in DMSO, 100mM) and 20% (v/v) MeOH

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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: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.86→45.69 Å / Num. obs: 39203 / % possible obs: 98 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.21 Å2 / Rsym value: 0.093 / Net I/σ(I): 12.76
Reflection shellResolution: 1.86→1.87 Å / Mean I/σ(I) obs: 2.59 / Num. unique obs: 5792 / Rsym value: 0.496

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Processing

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

1q8w


Resolution: 1.86→45.69 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.4907
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2264 1961 5 %
Rwork0.1867 37235 -
obs0.1887 39196 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.14 Å2
Refinement stepCycle: LAST / Resolution: 1.86→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 13 179 3022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00992915
X-RAY DIFFRACTIONf_angle_d1.01213953
X-RAY DIFFRACTIONf_chiral_restr0.0534426
X-RAY DIFFRACTIONf_plane_restr0.0069519
X-RAY DIFFRACTIONf_dihedral_angle_d18.32291032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.910.31421270.25732403X-RAY DIFFRACTION90.36
1.91-1.960.27621380.22352614X-RAY DIFFRACTION97.76
1.96-2.020.2491370.2142614X-RAY DIFFRACTION97.83
2.02-2.080.26031390.20012645X-RAY DIFFRACTION97.82
2.08-2.160.27481380.19482615X-RAY DIFFRACTION97.87
2.16-2.250.23371380.18162629X-RAY DIFFRACTION98.23
2.25-2.350.20851400.17522649X-RAY DIFFRACTION98.17
2.35-2.470.2271390.17982652X-RAY DIFFRACTION98.83
2.47-2.630.26331410.18442679X-RAY DIFFRACTION98.98
2.63-2.830.24971420.19522696X-RAY DIFFRACTION99.4
2.83-3.110.25881420.19492698X-RAY DIFFRACTION99.09
3.11-3.560.22771430.19062722X-RAY DIFFRACTION99.38
3.56-4.490.18341450.15812747X-RAY DIFFRACTION98.87
4.49-45.690.19411520.1872872X-RAY DIFFRACTION99.02
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.762950230190.6280850348252.066187125371.727803618931.928275107585.46494512386-0.0120420864967-0.136437315612-0.05170298462480.2013262048980.01962829729790.01025003350910.2888464979140.2412200550010.0594599718940.244991371833-0.05452515823710.03176088706250.3082795666870.04105533002330.288322835464-9.115827133929.19144332326-0.851069601263
22.68348832777-1.313112418981.258093575683.52621080028-0.6350344814342.0207350870.2938216494870.33053285147-0.127596727958-0.747368140102-0.03715737408130.5021279790.125411616716-0.170608916458-0.1954887044750.32364288825-0.0089599586888-0.07897523397730.3671287957170.02430865115250.375877354289-22.398381754417.4577809489-28.2396490888
31.108328613060.07100346848780.1128669254761.50655285736-0.5852080232221.347826485230.009132404838760.1012184127840.114572502013-0.1171608421550.0001805282743790.275787756917-0.0516790784963-0.2537708701520.03092598810210.1534709267550.0236145099123-0.001798888009140.160828978827-0.009185240159640.154072834799-7.8620070284223.3107319832-17.9976672953
41.69998352740.2440302497420.2598859968132.169569244320.07356297900241.90754747192-0.01324634773180.140090046615-0.123569589306-0.0731362744577-0.0533977782791-0.274142012230.08616906671720.1151579183850.05765823255460.1369286918270.02545956122470.01058425699010.1539200746220.005619189695840.1800461072365.636285816416.0280243797-18.1825643725
52.11168507173-0.3513167162041.212868205412.059023767670.009524919993451.74353187091-0.003790722530970.2542003306710.0897524241505-0.3659984059180.003899813847920.229313972086-0.186340633579-0.02756378114340.07148079258550.2494935819440.0115765205110.01531390664050.262435551393-0.008101373598480.291141116765-15.403442447524.6242521387-20.5593642958
68.266709188642.42564462685-0.7727074580567.050685229367.444583588719.372612364240.1390377460720.0107322552960.354096653856-0.274909967829-0.0940992365080.0101831829652-0.887441522770.231214140854-0.2118863194380.285725664991-0.02000902380360.00913758756090.28586746760.1343557552810.30092628645812.320521402433.6133193067-26.8890085722
79.104625713713.886289603090.4912950372512.73225355142-1.224728635572.221337795310.007451173682560.522782644571-0.174200583765-0.6739910151690.0396594648217-0.2093443606880.007938827231480.2049764332060.006112807597670.3081305917720.0409598253912-0.01732638835470.2837067137280.02127983169610.1826916051711.6279613991424.9514538965-31.6007117685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 114 )
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 179 )
4X-RAY DIFFRACTION4chain 'A' and (resid 180 through 297 )
5X-RAY DIFFRACTION5chain 'A' and (resid 298 through 350 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 12 )
7X-RAY DIFFRACTION7chain 'B' and (resid 13 through 22 )

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