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- PDB-5vhb: Crystal structure of Protein Kinase A in complex with the PKI pep... -

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Basic information

Entry
Database: PDB / ID: 5vhb
TitleCrystal structure of Protein Kinase A in complex with the PKI peptide and Aminobenzothiazole based inhibitor
Components
  • PKI peptide
  • cAMP-dependent protein kinase catalytic subunit alphaCAMP-dependent pathway
KeywordsTRANSFERASE / Kinase
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 / AURKA Activation by TPX2 / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / PKA activation / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / 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 / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / protein kinase A signaling / negative regulation of TORC1 signaling / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / protein kinase activity / protein domain specific binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / 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-9CY / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å
AuthorsJudge, R.A.
CitationJournal: Chembiochem / Year: 2018
Title: Design of Aminobenzothiazole Inhibitors of Rho Kinases 1 and 2 by Using Protein Kinase A as a Structure Surrogate.
Authors: Judge, R.A. / Vasudevan, A. / Scott, V.E. / Simler, G.H. / Pratt, S.D. / Namovic, M.T. / Putman, C.B. / Aguirre, A. / Stoll, V.S. / Mamo, M. / Swann, S.I. / Cassar, S.C. / Faltynek, C.R. / ...Authors: Judge, R.A. / Vasudevan, A. / Scott, V.E. / Simler, G.H. / Pratt, S.D. / Namovic, M.T. / Putman, C.B. / Aguirre, A. / Stoll, V.S. / Mamo, M. / Swann, S.I. / Cassar, S.C. / Faltynek, C.R. / Kage, K.L. / Boyce-Rustay, J.M. / Hobson, A.D.
History
DepositionApr 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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: PKI peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2233
Polymers42,8912
Non-polymers3321
Water8,935496
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-3 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.304, 75.981, 80.131
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: 40917.590 Da / Num. of mol.: 1 / Mutation: T198(TPO), S140(SEP), S339(SEP)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKACA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)T1R / References: UniProt: P00517, cAMP-dependent protein kinase
#2: Protein/peptide PKI peptide / PKI-alpha


Mass: 1973.177 Da / Num. of mol.: 1 / Fragment: UNP residues 6-23 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: Q3SX13
#3: Chemical ChemComp-9CY / N-[(2S)-1-hydroxy-3-phenylpropan-2-yl]-4-(pyridin-4-yl)benzamide


Mass: 332.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.73 Å3/Da / Density % sol: 55.02 % / Mosaicity: 0.11 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.6 / Details: 15% methanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→75.98 Å / Num. obs: 57161 / % possible obs: 98 % / Redundancy: 5.6 % / Biso Wilson estimate: 25.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 22
Reflection shellResolution: 1.61→1.7 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.451 / Num. unique obs: 7394 / CC1/2: 0.792 / Rpim(I) all: 0.296 / Rrim(I) all: 0.543 / % possible all: 87.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
Aimless0.5.12data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→23.57 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.087 / SU Rfree Blow DPI: 0.086 / SU Rfree Cruickshank DPI: 0.08
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2811 4.93 %RANDOM
Rwork0.177 ---
obs0.178 57068 97.4 %-
Displacement parametersBiso mean: 28.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.0653 Å20 Å20 Å2
2---3.9419 Å20 Å2
3---3.8766 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.61→23.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 56 496 3375
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012971HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.924024HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1031SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes454HARMONIC5
X-RAY DIFFRACTIONt_it2971HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion16.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion366SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3793SEMIHARMONIC4
LS refinement shellResolution: 1.61→1.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2591 153 4.67 %
Rwork0.2412 3120 -
all0.242 3273 -
obs--76.11 %

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