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- PDB-3agm: Complex of PKA with the bisubstrate protein kinase inhibitor ARC-670 -

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Basic information

Entry
Database: PDB / ID: 3agm
TitleComplex of PKA with the bisubstrate protein kinase inhibitor ARC-670
Components
  • N~2~-{8-OXO-8-[4-(9H-PURIN-6-YL)PIPERAZIN-1-YL]OCTANOYL}-D-ARGINYL-D-ARGINYL-D-ARGINYL-D-ARGINYL-D-ARGINYL-D-ARGININAMIDE
  • cAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PKA / protein kinase A / bisubstrate / bisubstrate inhibitor / ARC-670 / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Function / homology
Function and homology information


PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / channel activator activity / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / cell communication by electrical coupling involved in cardiac conduction / high-density lipoprotein particle assembly / nucleotide-activated protein kinase complex ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / channel activator activity / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / cell communication by electrical coupling involved in cardiac conduction / high-density lipoprotein particle assembly / nucleotide-activated protein kinase complex / Rap1 signalling / potassium channel inhibitor activity / histone H1-4S35 kinase activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / cellular response to parathyroid hormone stimulus / protein localization to lipid droplet / negative regulation of interleukin-2 production / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / dorsal/ventral neural tube patterning / PKA activation / Triglyceride catabolism / regulation of osteoblast differentiation / sperm capacitation / cellular response to cold / ciliary base / protein kinase A regulatory subunit binding / negative regulation of glycolytic process through fructose-6-phosphate / intracellular potassium ion homeostasis / RET signaling / mesoderm formation / Interleukin-3, Interleukin-5 and GM-CSF signaling / PKA activation in glucagon signalling / Regulation of MECP2 expression and activity / regulation of cardiac conduction / regulation of macroautophagy / plasma membrane raft / DARPP-32 events / cAMP/PKA signal transduction / regulation of cardiac muscle contraction / sperm flagellum / vascular endothelial cell response to laminar fluid shear stress / postsynaptic modulation of chemical synaptic transmission / renal water homeostasis / Hedgehog 'off' state / Ion homeostasis / negative regulation of protein localization to chromatin / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / protein serine/threonine/tyrosine kinase activity / cellular response to epinephrine stimulus / Recruitment of mitotic centrosome proteins and complexes / CD209 (DC-SIGN) signaling / protein export from nucleus / cellular response to glucagon stimulus / calcium channel complex / Recruitment of NuMA to mitotic centrosomes / Mitochondrial protein degradation / Anchoring of the basal body to the plasma membrane / positive regulation of calcium-mediated signaling / FCGR3A-mediated IL10 synthesis / positive regulation of gluconeogenesis / positive regulation of phagocytosis / regulation of heart rate / acrosomal vesicle / AURKA Activation by TPX2 / positive regulation of protein export from nucleus / regulation of microtubule cytoskeleton organization / negative regulation of smoothened signaling pathway / neuromuscular junction / neural tube closure / Regulation of insulin secretion / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / positive regulation of cholesterol biosynthetic process / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / VEGFA-VEGFR2 Pathway / mRNA processing / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cytokine-mediated signaling pathway / positive regulation of insulin secretion / Regulation of PLK1 Activity at G2/M Transition / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / manganese ion binding / GPER1 signaling / cellular response to heat / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Factors involved in megakaryocyte development and platelet production / sperm midpiece
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. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
INHIBITOR ARC-670 / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPflug, A. / Ragozina, J. / Uri, A. / Bossemeyer, D. / Engh, R.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Diversity of bisubstrate binding modes of adenosine analogue-oligoarginine conjugates in protein kinase a and implications for protein substrate interactions.
Authors: Pflug, A. / Rogozina, J. / Lavogina, D. / Enkvist, E. / Uri, A. / Engh, R.A. / Bossemeyer, D.
History
DepositionApr 2, 2010Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: 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 1.2Oct 5, 2011Group: Derived calculations
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
B: N~2~-{8-OXO-8-[4-(9H-PURIN-6-YL)PIPERAZIN-1-YL]OCTANOYL}-D-ARGINYL-D-ARGINYL-D-ARGINYL-D-ARGINYL-D-ARGINYL-D-ARGININAMIDE


Theoretical massNumber of molelcules
Total (without water)42,1102
Polymers42,1102
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.520, 85.520, 99.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 40808.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKACA, PRKACA / Plasmid: pET-285b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P17612, cAMP-dependent protein kinase
#2: Protein/peptide N~2~-{8-OXO-8-[4-(9H-PURIN-6-YL)PIPERAZIN-1-YL]OCTANOYL}-D-ARGINYL-D-ARGINYL-D-ARGINYL-D-ARGINYL-D-ARGINYL-D-ARGININAMIDE


Type: Peptide-like / Class: Inhibitor / Mass: 1301.581 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: INHIBITOR ARC-670
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25 mM Tris-HCl, 25 mM NaCl, 1.5 mM octanoyl-N-methylglucamide, equilibrated against 12-15 % (v/v) methanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.23985 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 2→51.61 Å / Num. all: 25525 / Num. obs: 25504 / % possible obs: 99.92 % / Redundancy: 7.7 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3656 / Rsym value: 0.393 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CDK

1cdk


Resolution: 2→51.61 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.903 / SU B: 10.556 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1297 5.1 %RANDOM
Rwork0.223 ---
all0.277 25469 --
obs0.225 24153 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2→51.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 0 118 3013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222970
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.9824003
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0515338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55824.126143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1415.029520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1931515
X-RAY DIFFRACTIONr_chiral_restr0.0820.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212264
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4961.51695
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.91822739
X-RAY DIFFRACTIONr_scbond_it1.53431275
X-RAY DIFFRACTIONr_scangle_it2.4964.51264
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 89 -
Rwork0.267 1761 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -22.624 Å / Origin y: 22.952 Å / Origin z: 4.846 Å
111213212223313233
T0.017 Å20.0063 Å20 Å2-0.0274 Å20.0133 Å2--0.0505 Å2
L1.8372 °2-0.5614 °2-0.2409 °2-2.4912 °2-0.1283 °2--1.8865 °2
S0.0151 Å °0.0708 Å °0.0747 Å °0.1307 Å °0.0313 Å °-0.0991 Å °-0.1399 Å °-0.0833 Å °-0.0464 Å °

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