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- PDB-6frx: PKA variant as Aurora B mimic in complex with a dianilinopyrimidi... -

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Basic information

Entry
Database: PDB / ID: 6frx
TitlePKA variant as Aurora B mimic in complex with a dianilinopyrimidine inhibitor
Components
  • cAMP-dependent protein kinase catalytic subunit alphaCAMP-dependent pathway
  • cAMP-dependent protein kinase inhibitor alphaCAMP-dependent pathway
KeywordsTRANSFERASE / Protein kinase / surrogate model / catalytic domain
Function / homology
Function and homology information


PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / mitochondrial protein catabolic process / ROBO receptors bind AKAP5 / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / negative regulation of cAMP-dependent protein kinase activity / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / mitochondrial protein catabolic process / ROBO receptors bind AKAP5 / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / negative regulation of cAMP-dependent protein kinase activity / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly / Rap1 signalling / renal water homeostasis / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cell communication by electrical coupling involved in cardiac conduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / Loss of phosphorylation of MECP2 at T308 / sperm capacitation / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / cAMP-dependent protein kinase activity / ciliary base / cAMP-dependent protein kinase complex / negative regulation of glycolytic process through fructose-6-phosphate / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / Triglyceride catabolism / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / plasma membrane raft / PKA activation in glucagon signalling / : / Regulation of MECP2 expression and activity / mesoderm formation / regulation of cardiac conduction / RET signaling / DARPP-32 events / Interleukin-3, Interleukin-5 and GM-CSF signaling / sperm flagellum / Mitochondrial protein degradation / regulation of macroautophagy / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / negative regulation of TORC1 signaling / protein kinase A signaling / Recruitment of NuMA to mitotic centrosomes / cellular response to epinephrine stimulus / calcium channel complex / Anchoring of the basal body to the plasma membrane / regulation of cytosolic calcium ion concentration / regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / regulation of heart rate / CD209 (DC-SIGN) signaling / AURKA Activation by TPX2 / FCGR3A-mediated IL10 synthesis / positive regulation of protein export from nucleus / acrosomal vesicle / Regulation of insulin secretion / neural tube closure / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / Vasopressin regulates renal water homeostasis via Aquaporins / cytokine-mediated signaling pathway / VEGFA-VEGFR2 Pathway / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Regulation of PLK1 Activity at G2/M Transition / cellular response to heat / manganese ion binding / Factors involved in megakaryocyte development and platelet production / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle
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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-E3Z / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsEngh, R.A. / Kazi, A.A.
CitationJournal: To Be Published
Title: PKA variant as Aurora B mimic in complex with a dianilinopyrimidine inhibitor
Authors: Engh, R.A. / Kazi, A.A.
History
DepositionFeb 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release

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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)43,4493
Polymers43,0832
Non-polymers3661
Water4,702261
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-5 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.743, 77.784, 96.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40856.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKACA, PKACA / Production host: Escherichia coli (E. coli) / References: UniProt: P17612, cAMP-dependent protein kinase
#2: Protein/peptide cAMP-dependent protein kinase inhibitor alpha / CAMP-dependent pathway / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 2226.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61925
#3: Chemical ChemComp-E3Z / ~{N}-[3-[(5-chloranyl-2-phenylazanyl-pyrimidin-4-yl)amino]phenyl]prop-2-enamide


Mass: 365.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16ClN5O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PKA-AU6 at 10mg/ml in 25mM BisTRIS/HCl (pH7.0), 150mM KCl, 1.5mM octanoyl-N-methylglucamide and 0.8mM PKI was equilibrated against 12-26% (v/v) methanol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.88→46.9 Å / Num. obs: 36422 / % possible obs: 99 % / Redundancy: 4.7 % / Net I/σ(I): 12.5
Reflection shellResolution: 1.88→1.95 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→46.9 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.47
RfactorNum. reflection% reflection
Rfree0.2264 1822 5 %
Rwork0.1895 --
obs0.1914 36420 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.88→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 26 261 3194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073008
X-RAY DIFFRACTIONf_angle_d0.9014063
X-RAY DIFFRACTIONf_dihedral_angle_d13.0881775
X-RAY DIFFRACTIONf_chiral_restr0.051423
X-RAY DIFFRACTIONf_plane_restr0.005518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.879-1.92980.40621370.34692584X-RAY DIFFRACTION98
1.9298-1.98660.29881390.2922654X-RAY DIFFRACTION100
1.9866-2.05070.34081370.26382608X-RAY DIFFRACTION99
2.0507-2.1240.2711390.22932632X-RAY DIFFRACTION100
2.124-2.20910.24771400.21752657X-RAY DIFFRACTION100
2.2091-2.30960.25511390.20512644X-RAY DIFFRACTION99
2.3096-2.43140.27381400.19552651X-RAY DIFFRACTION100
2.4314-2.58370.24811390.19572641X-RAY DIFFRACTION99
2.5837-2.78320.22531410.20262678X-RAY DIFFRACTION100
2.7832-3.06320.24391410.19462679X-RAY DIFFRACTION100
3.0632-3.50630.24591400.18742665X-RAY DIFFRACTION99
3.5063-4.41710.19111430.1542725X-RAY DIFFRACTION99
4.4171-48.25790.16941470.16412780X-RAY DIFFRACTION97

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