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- PDB-1q8u: The Catalytic Subunit of cAMP-dependent Protein Kinase in Complex... -

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Basic information

Entry
Database: PDB / ID: 1q8u
TitleThe Catalytic Subunit of cAMP-dependent Protein Kinase in Complex with Rho-kinase Inhibitor H-1152P
Components
  • cAMP-dependent protein kinase inhibitor, alpha form
  • cAMP-dependent protein kinase, alpha-catalytic subunit
KeywordsTransferase/Transferase Inhibitor / KINASE-INHIBITOR-COMPLEX / PHOSPHOTRANSFERASE/INHIBITOR / CAMP / PHOSPHORYLATION / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / PKA / RHO-KINASE / Transferase-Transferase Inhibitor COMPLEX
Function / homology
Function and homology information


CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production ...CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / RET signaling / AURKA Activation by TPX2 / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / negative regulation of cAMP-dependent protein kinase activity / negative regulation of cAMP/PKA signal transduction / PKA activation / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Mitochondrial protein degradation / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / protein kinase A signaling / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / protein kinase activity / protein phosphorylation / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
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-H52 / N-OCTANOYL-N-METHYLGLUCAMINE / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBreitenlechner, C. / Gassel, M. / Hidaka, H. / Kinzel, V. / Huber, R. / Engh, R.A. / Bossemeyer, D.
CitationJournal: Structure / Year: 2003
Title: Protein kinase A in complex with Rho-kinase inhibitors Y-27632, Fasudil, and H-1152P: structural basis of selectivity.
Authors: Breitenlechner, C. / Gassel, M. / Hidaka, H. / Kinzel, V. / Huber, R. / Engh, R.A. / Bossemeyer, D.
History
DepositionAug 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP-dependent protein kinase, alpha-catalytic subunit
B: cAMP-dependent protein kinase inhibitor, alpha form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9735
Polymers43,0132
Non-polymers9603
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint4 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.220, 76.422, 81.790
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, alpha-catalytic subunit / PKA C-alpha / PROTEIN KINASE A


Mass: 40786.395 Da / Num. of mol.: 1 / Fragment: Catalytic Subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKACA / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P00517, EC: 2.7.1.37
#2: Protein/peptide cAMP-dependent protein kinase inhibitor, alpha form / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: residues 5-24 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. / References: UniProt: P04541, UniProt: P63249*PLUS
#3: Chemical ChemComp-H52 / (S)-2-METHYL-1-[(4-METHYL-5-ISOQUINOLINE)SULFONYL]-HOMOPIPERAZINE


Mass: 319.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O2S
#4: Chemical ChemComp-MG8 / N-OCTANOYL-N-METHYLGLUCAMINE / MEGA 8, N-(D-GLUCITYL)-N-METHYLOCTANAMIDE


Mass: 321.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H31NO6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: LiCl, MesBisTris, methanol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
175 mM1dropLiCl
225 mMMES-bis-tris1droppH6.4
315 %methanol1reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Aug 4, 2000 / Details: GRAPHITE MONOCHROMATOR
RadiationMonochromator: GRAPHITE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→10.91 Å / Num. all: 37060 / Num. obs: 34029 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→2 Å / % possible all: 56
Reflection
*PLUS
Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 56 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
ASTROdata reduction
SAINTdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→10.91 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.265 / SU ML: 0.092 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.139 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1702 5 %RANDOM
Rwork0.171 ---
all0.173 34029 --
obs0.173 32327 91.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.698 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.2 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 52 232 3301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213091
X-RAY DIFFRACTIONr_bond_other_d0.0020.022736
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9614187
X-RAY DIFFRACTIONr_angle_other_deg1.11536338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.495362
X-RAY DIFFRACTIONr_chiral_restr0.1010.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023409
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02666
X-RAY DIFFRACTIONr_nbd_refined0.2050.2504
X-RAY DIFFRACTIONr_nbd_other0.2360.22807
X-RAY DIFFRACTIONr_nbtor_other0.0870.21653
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.340.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.211
X-RAY DIFFRACTIONr_mcbond_it0.9191.51810
X-RAY DIFFRACTIONr_mcangle_it1.69622915
X-RAY DIFFRACTIONr_scbond_it2.37831281
X-RAY DIFFRACTIONr_scangle_it3.824.51272
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 88
Rwork0.282 1583
Refinement
*PLUS
Highest resolution: 1.9 Å / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.491

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