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- PDB-5bx7: PKA in complex with a benzothiophene fragment compound. -

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Basic information

Entry
Database: PDB / ID: 5bx7
TitlePKA in complex with a benzothiophene fragment compound.
Components(cAMP-dependent protein kinase ...) x 2
KeywordsTRANSFERASE / Inhibitor / protein kinase / structure-guided / fragment-based
Function / homology
Function and homology information


PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / negative regulation of cAMP-dependent protein kinase activity / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / HDL assembly / mitochondrial protein catabolic process / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / negative regulation of cAMP-dependent protein kinase activity / regulation of protein binding / nucleotide-activated protein kinase complex / high-density lipoprotein particle assembly / Rap1 signalling / renal water homeostasis / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cell communication by electrical coupling involved in cardiac conduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / Loss of phosphorylation of MECP2 at T308 / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / sperm capacitation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / Triglyceride catabolism / protein kinase A regulatory subunit binding / plasma membrane raft / protein kinase A catalytic subunit binding / PKA activation in glucagon signalling / : / Regulation of MECP2 expression and activity / mesoderm formation / RET signaling / DARPP-32 events / Interleukin-3, Interleukin-5 and GM-CSF signaling / regulation of cardiac muscle contraction / regulation of cardiac conduction / sperm flagellum / regulation of macroautophagy / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of gluconeogenesis / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / protein kinase A signaling / Mitochondrial protein degradation / calcium channel complex / Anchoring of the basal body to the plasma membrane / cellular response to epinephrine stimulus / regulation of cytosolic calcium ion concentration / regulation of G2/M transition of mitotic cell cycle / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / regulation of heart rate / CD209 (DC-SIGN) signaling / AURKA Activation by TPX2 / FCGR3A-mediated IL10 synthesis / positive regulation of protein export from nucleus / acrosomal vesicle / neural tube closure / Regulation of insulin secretion / cellular response to glucose stimulus / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / cytokine-mediated signaling pathway / VEGFA-VEGFR2 Pathway / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Regulation of PLK1 Activity at G2/M Transition / Factors involved in megakaryocyte development and platelet production / cellular response to heat / manganese ion binding / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle
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
1-benzothiophen-3-ylmethanol / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsNarayanan, D. / Alam, K.A. / Engh, R.A.
Funding support Norway, 1items
OrganizationGrant numberCountry
FRINAT191303 Norway
CitationJournal: To Be Published
Title: PKA based studies of ligand interactions with a methionine gatekeeper.
Authors: Narayanan, D. / Gani, O.A. / Alam, K.A. / Engh, R.A.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5786
Polymers43,1152
Non-polymers4634
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-16 kcal/mol
Surface area16700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.653, 75.417, 80.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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CAMP-dependent protein kinase ... , 2 types, 2 molecules AB

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


Mass: 40888.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKACA, PKACA / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PRAR / References: UniProt: P17612, cAMP-dependent protein kinase
#2: Protein/peptide cAMP-dependent protein kinase inhibitor alpha / PKI-alpha / cAMP-dependent protein kinase inhibitor / muscle/brain isoform


Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: UNP residues 6-25 / Source method: obtained synthetically / Details: UNP residues 6-25 / Source: (synth.) Homo sapiens (human) / References: UniProt: P61925

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Non-polymers , 4 types, 206 molecules

#3: Chemical ChemComp-4W1 / 1-benzothiophen-3-ylmethanol


Mass: 164.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8OS
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The droplets, containing 10 mg/ml PKA. 25 mM Bis-Tris-HCl, pH 7.0, 150 mM KCl, 1.5mM octanoyl-N-methylglucamide and 0.8 mM PKI peptide, were equilibrated against 12-26 % (v/v) methanol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.89→37.71 Å / Num. all: 35550 / Num. obs: 35516 / % possible obs: 98.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 1.8 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Coot0.8.2model building
MOLREP11phasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VQH

3vqh


Resolution: 1.89→37.71 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 1838 5.18 %Random selection
Rwork0.1751 ---
obs0.1777 35516 98.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.89→37.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 31 202 3243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073146
X-RAY DIFFRACTIONf_angle_d1.0594245
X-RAY DIFFRACTIONf_dihedral_angle_d14.831177
X-RAY DIFFRACTIONf_chiral_restr0.042441
X-RAY DIFFRACTIONf_plane_restr0.005539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8888-1.93990.31881100.24862393X-RAY DIFFRACTION91
1.9399-1.9970.31321280.2452562X-RAY DIFFRACTION99
1.997-2.06140.28961330.22552585X-RAY DIFFRACTION99
2.0614-2.13510.26871350.20532609X-RAY DIFFRACTION99
2.1351-2.22060.23641280.19212593X-RAY DIFFRACTION99
2.2206-2.32160.23251500.18242581X-RAY DIFFRACTION99
2.3216-2.4440.27041590.18572608X-RAY DIFFRACTION100
2.444-2.59710.23371730.17932561X-RAY DIFFRACTION99
2.5971-2.79760.22461250.18862628X-RAY DIFFRACTION99
2.7976-3.0790.22521620.17822571X-RAY DIFFRACTION99
3.079-3.52430.22321580.17642601X-RAY DIFFRACTION99
3.5243-4.43910.21171320.14012669X-RAY DIFFRACTION98
4.4391-37.710.16031450.14172717X-RAY DIFFRACTION96
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)
11.0601-0.176-0.10651.92250.42322.4642-0.01190.0222-0.1276-0.0822-0.02120.25280.2243-0.28170.01720.09250.0101-0.01770.24210.00610.2266-36.28356.0184-9.4256
23.62460.7462-2.31711.082-0.63053.29990.0611-0.19030.33890.1550.03830.0586-0.3311-0.0778-0.03660.14560.029-0.01390.203-0.01660.2008-30.255119.59130.0214
30.5211-0.3069-0.0981.0801-0.42961.4094-0.0505-0.0260.01430.04490.04820.08770.0757-0.2028-0.00250.0975-0.00510.00110.1626-0.02450.1475-30.34114.4105-2.2068
41.4077-0.0577-0.04111.5372-0.55162.2195-0.01110.01-0.19430-0.0223-0.00790.4584-0.0320.02730.2067-0.00990.01290.115-0.01830.1259-23.4602-8.2721-2.4403
50.6742-0.2338-0.26092.9899-1.54193.54710.0189-0.18080.17040.3708-0.0024-0.1546-0.4450.0318-0.02050.15270.0262-0.02450.2359-0.04160.2574-26.84819.92241.6561
63.25290.03692.37229.7732-2.44153.3809-0.08390.08560.01110.1939-0.20720.34160.1951-0.15640.33690.18490.04260.04350.2134-0.0190.134-13.0323-8.176216.1225
75.9296-1.43541.7673.5050.40664.7494-0.19630.11730.4157-0.31860.0326-0.4431-0.53660.07820.16470.2604-0.00980.00420.1251-0.00420.1794-13.8863.72374.4123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 160 )
4X-RAY DIFFRACTION4chain 'A' and (resid 161 through 316 )
5X-RAY DIFFRACTION5chain 'A' and (resid 317 through 350 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 11 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 24 )

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