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- PDB-3bwj: Complex of PKA with the bisubstrate protein kinase inhibitor lead... -

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Basic information

Entry
Database: PDB / ID: 3bwj
TitleComplex of PKA with the bisubstrate protein kinase inhibitor lead compound Arc-1034
ComponentscAMP-dependent protein kinase, alpha-catalytic subunit
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / bisubstrate inhibitor / protein kinase / Serine/threonine-protein kinase / ATP-binding / cAMP / Phosphoprotein / 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 / 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 / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / AMP-activated protein kinase activity / Vasopressin regulates renal water homeostasis via Aquaporins / Mitochondrial protein degradation / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / protein kinase A 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 / cytoplasm / cytosol
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. / 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. ...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
ARC-1034 / Chem-ARX / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLavogina, D. / Koenig, N. / Uri, A. / Bossemeyer, D.
Citation
Journal: J.Med.Chem. / Year: 2009
Title: Structural analysis of ARC-type inhibitor (ARC-1034) binding to protein kinase A catalytic subunit and rational design of bisubstrate analogue inhibitors of basophilic protein kinases.
Authors: Lavogina, D. / Lust, M. / Viil, I. / Konig, N. / Raidaru, G. / Rogozina, J. / Enkvist, E. / Uri, A. / Bossemeyer, D.
#1: Journal: J.Med.Chem. / Year: 2006
Title: Conjugation of Adenosine and Hexa-(D-arginine)Leads to a Nanomolar Bisubstrate-Analog Inhibitor of Basophilic Protein Kinases
Authors: Enkvist, E. / Lavogina, D. / Raidaru, G. / Vaasa, A. / Viil, I. / Lust, M. / Viht, K. / Uri, A.
History
DepositionJan 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Sep 4, 2019Group: Data collection / Derived calculations / Category: reflns / reflns_shell / struct_conn
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value ..._reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _reflns.pdbx_redundancy / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value / _struct_conn.pdbx_leaving_atom_flag

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1983
Polymers40,7861
Non-polymers1,4122
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.188, 72.632, 77.221
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


Mass: 40786.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKACA / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P00517, cAMP-dependent protein kinase
#2: Chemical ChemComp-ARX / (2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-N-(6-{[(1R)-4-carbamimidamido-1-{[(1R)-4-carbamimidamido-1-carbamoylbutyl]carbamoyl}butyl]amino}-6-oxohexyl)-3,4-dihydroxytetrahydrofuran-2-carboxamide / ARC-1034


Type: peptide-like, Non-polymer / Class: Inhibitor / Mass: 705.769 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H47N15O7 / References: ARC-1034
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Mes-Bis-Tris, LiCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.3→52.926 Å / Num. all: 17407 / Num. obs: 18346 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.9 / Biso Wilson estimate: 32.7 Å2 / Rsym value: 0.119 / Net I/σ(I): 0
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 1.05 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1340 / Rsym value: 0.387 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→52.926 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.106 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.366 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 939 5.1 %RANDOM
Rwork0.19899 ---
obs0.20145 17407 99.87 %-
all-0 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.59 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.3→52.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 100 175 3098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223000
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9944051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9845340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11124.247146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.21215.057523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.161515
X-RAY DIFFRACTIONr_chiral_restr0.1150.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022266
X-RAY DIFFRACTIONr_nbd_refined0.2010.21322
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21981
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2185
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3890.218
X-RAY DIFFRACTIONr_mcbond_it1.0551.51754
X-RAY DIFFRACTIONr_mcangle_it1.64822745
X-RAY DIFFRACTIONr_scbond_it2.49131436
X-RAY DIFFRACTIONr_scangle_it3.8434.51306
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 66 -
Rwork0.223 1274 -
obs-1340 100 %

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