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- PDB-5n3e: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -

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Basic information

Entry
Database: PDB / ID: 5n3e
TitlecAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule 6-dimethylaminopyridine-3-carboxylic acid
Components(cAMP-dependent protein kinase ...) x 2
KeywordsTRANSFERASE / fragment / complex / serine threonine kinase / cAMP / kinase / PKA
Function / homology
Function and homology information


negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus ...negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus / regulation of osteoblast differentiation / cellular response to cold / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / mesoderm formation / plasma membrane raft / axoneme / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / regulation of G2/M transition of mitotic cell cycle / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / acrosomal vesicle / protein export from nucleus / positive regulation of phagocytosis / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / 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 / mRNA processing / adenylate cyclase-activating G protein-coupled receptor signaling pathway / manganese ion binding / cellular response to heat / postsynapse / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / centrosome / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol
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. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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. / 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
6-(dimethylamino)pyridine-3-carboxylic acid / cAMP-dependent protein kinase inhibitor / UPF0418 protein FAM164A / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.529 Å
AuthorsSiefker, C. / Heine, A. / Klebe, G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Fragment Binding to Kinase Hinge: If Charge Distribution and Local pK a Shifts Mislead Popular Bioisosterism Concepts.
Authors: Oebbeke, M. / Siefker, C. / Wagner, B. / Heine, A. / Klebe, G.
History
DepositionFeb 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.2Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 17, 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5505
Polymers43,1872
Non-polymers3623
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-10 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.631, 72.297, 108.576
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: 41193.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Phosphorylation of S11, S140, T198 and S339 / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide cAMP-dependent protein kinase inhibitor


Mass: 1993.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cAMP dependent protein kinase inhibitor peptide / Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: A0A061IH64, UniProt: G3HK48*PLUS

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Non-polymers , 4 types, 244 molecules

#3: Chemical ChemComp-46L / 6-(dimethylamino)pyridine-3-carboxylic acid


Mass: 166.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N2O2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.83 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: MES-BIS-TRIS Mega8-Solution DTT EDTA LiCl Methanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2016 / Details: Silicon, active surface
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 69062 / % possible obs: 98 % / Redundancy: 7.13 % / CC1/2: 0.99 / Rrim(I) all: 0.045 / Net I/σ(I): 23.19
Reflection shellResolution: 1.53→1.62 Å / Redundancy: 7.28 % / Mean I/σ(I) obs: 3.46 / Num. unique obs: 10849 / CC1/2: 0.91 / Rrim(I) all: 0.547 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WIH

4wih


Resolution: 1.529→45.538 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1846 3454 5 %
Rwork0.155 --
obs0.1565 69050 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.529→45.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 24 241 3146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063060
X-RAY DIFFRACTIONf_angle_d0.8164158
X-RAY DIFFRACTIONf_dihedral_angle_d14.9771812
X-RAY DIFFRACTIONf_chiral_restr0.051439
X-RAY DIFFRACTIONf_plane_restr0.006544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.529-1.550.2531320.21522505X-RAY DIFFRACTION94
1.55-1.57210.22911350.19872567X-RAY DIFFRACTION96
1.5721-1.59560.23691350.17692562X-RAY DIFFRACTION97
1.5956-1.62050.18521360.16612568X-RAY DIFFRACTION97
1.6205-1.64710.20591340.15442562X-RAY DIFFRACTION97
1.6471-1.67550.22451360.15352570X-RAY DIFFRACTION97
1.6755-1.7060.18081350.1412564X-RAY DIFFRACTION98
1.706-1.73880.17261370.13132614X-RAY DIFFRACTION97
1.7388-1.77430.16541350.12882571X-RAY DIFFRACTION98
1.7743-1.81290.20751380.1342615X-RAY DIFFRACTION98
1.8129-1.8550.1911350.13372565X-RAY DIFFRACTION98
1.855-1.90140.1661390.13872637X-RAY DIFFRACTION98
1.9014-1.95280.18491370.14682599X-RAY DIFFRACTION98
1.9528-2.01030.16941370.14212615X-RAY DIFFRACTION98
2.0103-2.07520.16111380.14222606X-RAY DIFFRACTION98
2.0752-2.14940.19061380.14442626X-RAY DIFFRACTION99
2.1494-2.23540.19161380.14082617X-RAY DIFFRACTION97
2.2354-2.33710.17781380.13942640X-RAY DIFFRACTION98
2.3371-2.46040.17751410.14392667X-RAY DIFFRACTION99
2.4604-2.61450.17231380.14862628X-RAY DIFFRACTION99
2.6145-2.81630.17391420.15922690X-RAY DIFFRACTION99
2.8163-3.09970.21981420.16092695X-RAY DIFFRACTION99
3.0997-3.54810.17641420.16052697X-RAY DIFFRACTION99
3.5481-4.46960.17571450.15142756X-RAY DIFFRACTION99
4.4696-45.55850.18771510.17892860X-RAY DIFFRACTION99

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