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- PDB-3agl: Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1039 -

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Basic information

Entry
Database: PDB / ID: 3agl
TitleComplex of PKA with the bisubstrate protein kinase inhibitor ARC-1039
ComponentscAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PKA / protein kinase A / bisubstrate inhibitor / ARC-1039 / 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 / nucleotide-activated protein kinase complex / cell communication by electrical coupling involved in cardiac conduction / high-density lipoprotein particle assembly ...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 / nucleotide-activated protein kinase complex / cell communication by electrical coupling involved in cardiac conduction / high-density lipoprotein particle assembly / Rap1 signalling / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / Loss of phosphorylation of MECP2 at T308 / protein localization to lipid droplet / CREB1 phosphorylation through the activation of Adenylate Cyclase / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / cellular response to parathyroid hormone stimulus / PKA activation / negative regulation of interleukin-2 production / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / Triglyceride catabolism / protein kinase A regulatory subunit binding / intracellular potassium ion homeostasis / mesoderm formation / RET signaling / cAMP/PKA signal transduction / Regulation of MECP2 expression and activity / Interleukin-3, Interleukin-5 and GM-CSF signaling / plasma membrane raft / PKA activation in glucagon signalling / DARPP-32 events / regulation of proteasomal protein catabolic process / regulation of cardiac conduction / regulation of cardiac muscle contraction / regulation of macroautophagy / sperm flagellum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / postsynaptic modulation of chemical synaptic transmission / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / Hedgehog 'off' state / Ion homeostasis / sperm midpiece / negative regulation of TORC1 signaling / cellular response to epinephrine stimulus / calcium channel complex / positive regulation of gluconeogenesis / Mitochondrial protein degradation / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / CD209 (DC-SIGN) signaling / Recruitment of mitotic centrosome proteins and complexes / acrosomal vesicle / positive regulation of calcium-mediated signaling / regulation of heart rate / FCGR3A-mediated IL10 synthesis / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of phagocytosis / protein export from nucleus / AURKA Activation by TPX2 / positive regulation of protein export from nucleus / Degradation of GLI1 by the proteasome / negative regulation of smoothened signaling pathway / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / neural tube closure / Regulation of insulin secretion / neuromuscular junction / cellular response to glucose stimulus / positive regulation of cholesterol biosynthetic process / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / peptidyl-serine phosphorylation / VEGFA-VEGFR2 Pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / cytokine-mediated signaling pathway / 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 / GPER1 signaling / manganese ion binding / cellular response to heat / Factors involved in megakaryocyte development and platelet production / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / protein phosphorylation / postsynapse / protein kinase activity
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
ARC-1039 / Chem-A03 / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Dec 12, 2012Group: Other
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5574
Polymers81,7772
Non-polymers1,7802
Water4,234235
1
A: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7792
Polymers40,8891
Non-polymers8901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7792
Polymers40,8891
Non-polymers8901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.180, 105.170, 106.470
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 / PKA C-alpha


Mass: 40888.547 Da / Num. of mol.: 2
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: Chemical ChemComp-A03 / (10R,20R,23R)-1-[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-20,23-bis(3-carbamimidamido propyl)-10-methyl-1,8,11,18,21-pentaoxo-2,9,12,19,22-pentaazatetracosan-24-amide / ARC-1039


Type: peptide-like, Non-polymer / Class: Inhibitor / Mass: 890.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H63N17O9 / References: ARC-1039
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 80 mM Mes-BisTris, 75 mM LiCl, 1.5 mM octanoyl-N-methylglucamide; mixed 2:1 with and equilibrated against 40%(v/v) MPD, pH 6.9, 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: 2.1→52.32 Å / Num. all: 48725 / Num. obs: 48701 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 4 / Num. unique all: 7001 / Rsym value: 0.413 / % 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: 2.1→52.32 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.216 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2459 5.1 %RANDOM
Rwork0.198 ---
obs0.2 46179 99.95 %-
all-48661 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.1→52.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5607 0 126 235 5968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225883
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.9777939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3615676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06124.126286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52915.0431040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7371530
X-RAY DIFFRACTIONr_chiral_restr0.0910.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214456
X-RAY DIFFRACTIONr_mcbond_it0.6971.53390
X-RAY DIFFRACTIONr_mcangle_it1.32325478
X-RAY DIFFRACTIONr_scbond_it2.0232493
X-RAY DIFFRACTIONr_scangle_it3.3154.52461
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 185 -
Rwork0.222 3351 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7220.06360.11152.2964-0.92191.1376-0.02280.06480.0415-0.0506-0.0318-0.1704-0.09710.08430.05470.0221-0.00360.01110.07270.00620.0281-11.0430.1727.872
21.1787-0.00450.21262.4223-0.49260.776-0.01140.09870.1863-0.0641-0.0147-0.0565-0.09870.00970.02620.0209-0.00180.0030.05240.0150.0313-11.25950.033-25.233
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2A - B-10 - 9999

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