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- PDB-5izj: Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1411 -

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Basic information

Entry
Database: PDB / ID: 5izj
TitleComplex of PKA with the bisubstrate protein kinase inhibitor ARC-1411
Components
  • 47P-AZ1-DAR-DAR
  • 47P-AZ1-DAR-DAR-DAR
  • cAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / protein kinase / inhibitor / bisubstrate / oligoarginine / PKA
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
4-(piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine / PHOSPHATE ION / polypeptide(D) / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPflug, A. / Enkvist, E. / Uri, A. / Engh, R.A.
CitationJournal: Bioconjug.Chem. / Year: 2016
Title: Bifunctional Ligands for Inhibition of Tight-Binding Protein-Protein Interactions.
Authors: Ivan, T. / Enkvist, E. / Viira, B. / Manoharan, G.B. / Raidaru, G. / Pflug, A. / Alam, K.A. / Zaccolo, M. / Engh, R.A. / Uri, A.
History
DepositionMar 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 2.0Jun 19, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_seq_map_depositor_info / pdbx_solvent_atom_site_mapping / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_auth_asym_id / _atom_site.pdbx_auth_atom_name / _atom_site.pdbx_auth_comp_id / _atom_site.pdbx_auth_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_solvent_atom_site_mapping.auth_seq_id / _pdbx_solvent_atom_site_mapping.label_asym_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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: cAMP-dependent protein kinase catalytic subunit alpha
G: 47P-AZ1-DAR-DAR
F: 47P-AZ1-DAR-DAR-DAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,99432
Polymers83,1184
Non-polymers2,87628
Water11,007611
1
A: cAMP-dependent protein kinase catalytic subunit alpha
G: 47P-AZ1-DAR-DAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,91816
Polymers41,4802
Non-polymers1,43814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cAMP-dependent protein kinase catalytic subunit alpha
F: 47P-AZ1-DAR-DAR-DAR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,07516
Polymers41,6382
Non-polymers1,43814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.940, 84.990, 77.010
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 40808.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKACA, PKACA / Production host: Escherichia coli (E. coli) / References: UniProt: P17612, cAMP-dependent protein kinase

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Polypeptide(D) , 2 types, 2 molecules GF

#2: Polypeptide(D) 47P-AZ1-DAR-DAR


Mass: 671.861 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: C61H112N32O9 please find a complete description of the molecule in the LIGAND section
Source: (synth.) Homo sapiens (human)
#3: Polypeptide(D) 47P-AZ1-DAR-DAR-DAR


Mass: 829.055 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: C61H112N32O9 please find a complete description of the molecule in the LIGAND section
Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 639 molecules

#4: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-6J9 / 4-(piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine


Mass: 203.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.4M lithium sulfate, 0.1M phosphate citrate pH 4.5, 17%-19% PEG 1.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.884
11-h,-k,l20.116
ReflectionResolution: 1.85→50 Å / Num. obs: 65758 / % possible obs: 93.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 13.67
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.903

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→42.6 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.715 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.029 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22585 3209 4.9 %RANDOM
Rwork0.19708 ---
obs0.1985 62528 93.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.696 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å2-0 Å22.22 Å2
2--8.04 Å20 Å2
3----6.63 Å2
Refinement stepCycle: 1 / Resolution: 1.85→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5553 0 162 611 6326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195904
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2452.0027984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1055671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1223.993278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.014151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0951530
X-RAY DIFFRACTIONr_chiral_restr0.0850.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214405
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_it0.6851.9382673
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2252.8933334
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.6772.1783231
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.57917.1079682
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 160 -
Rwork0.306 3049 -
obs--62 %

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