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- PDB-5n33: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -

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Basic information

Entry
Database: PDB / ID: 5n33
TitlecAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule 3-amino-5-(trifluoromethyl)-1H-pyridin-2-one
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 / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / 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 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / 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
3-azanyl-5-(trifluoromethyl)-1~{H}-pyridin-2-one / 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: 1.434 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 1.0Feb 28, 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 16, 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 alpha-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5615
Polymers43,1872
Non-polymers3743
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-13 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.225, 72.589, 108.793
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 / Plasmid: pET-16bTEV / 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 alpha-like protein


Mass: 1993.318 Da / Num. of mol.: 1 / Fragment: UNP residues 12-30 / 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, 326 molecules

#3: Chemical ChemComp-8JW / 3-azanyl-5-(trifluoromethyl)-1~{H}-pyridin-2-one


Mass: 178.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5F3N2O
#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: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: Mar 13, 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: 1.43→50 Å / Num. obs: 84316 / % possible obs: 99.2 % / Redundancy: 6.25 % / CC1/2: 0.99 / Rrim(I) all: 0.066 / Net I/σ(I): 14.92
Reflection shellResolution: 1.43→1.52 Å / Redundancy: 6.23 % / Mean I/σ(I) obs: 2.64 / Num. unique obs: 12943 / CC1/2: 0.9 / Rrim(I) all: 0.526 / % possible all: 95.3

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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: 1.434→41.913 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1737 4216 5 %
Rwork0.1504 --
obs0.1515 84308 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.434→41.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 24 323 3228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083171
X-RAY DIFFRACTIONf_angle_d1.0024325
X-RAY DIFFRACTIONf_dihedral_angle_d18.9661164
X-RAY DIFFRACTIONf_chiral_restr0.077462
X-RAY DIFFRACTIONf_plane_restr0.007565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4345-1.45080.27361080.21352064X-RAY DIFFRACTION77
1.4508-1.46790.21371390.17852626X-RAY DIFFRACTION100
1.4679-1.48580.21121410.16872685X-RAY DIFFRACTION100
1.4858-1.50460.19971390.15742647X-RAY DIFFRACTION100
1.5046-1.52440.22321420.16582695X-RAY DIFFRACTION100
1.5244-1.54530.18411390.14942630X-RAY DIFFRACTION100
1.5453-1.56730.1741390.15362653X-RAY DIFFRACTION100
1.5673-1.59070.19381400.142652X-RAY DIFFRACTION100
1.5907-1.61560.16381420.13722699X-RAY DIFFRACTION100
1.6156-1.64210.15831380.13152633X-RAY DIFFRACTION100
1.6421-1.67040.16481420.13572685X-RAY DIFFRACTION100
1.6704-1.70080.14881410.12952685X-RAY DIFFRACTION100
1.7008-1.73350.1851400.13082650X-RAY DIFFRACTION100
1.7335-1.76890.15591400.12932677X-RAY DIFFRACTION100
1.7689-1.80730.17811400.13492654X-RAY DIFFRACTION100
1.8073-1.84940.18751410.13712674X-RAY DIFFRACTION100
1.8494-1.89560.14881420.14192692X-RAY DIFFRACTION100
1.8956-1.94690.18231400.14112678X-RAY DIFFRACTION100
1.9469-2.00410.16191410.14252662X-RAY DIFFRACTION100
2.0041-2.06880.1741420.1482706X-RAY DIFFRACTION100
2.0688-2.14280.17181420.14312693X-RAY DIFFRACTION100
2.1428-2.22860.16751410.13722682X-RAY DIFFRACTION100
2.2286-2.330.1531420.13622710X-RAY DIFFRACTION100
2.33-2.45280.15991420.13822688X-RAY DIFFRACTION100
2.4528-2.60650.15181420.14652704X-RAY DIFFRACTION100
2.6065-2.80770.18581440.15892728X-RAY DIFFRACTION100
2.8077-3.09010.18121430.15942717X-RAY DIFFRACTION100
3.0901-3.53710.18591450.16352749X-RAY DIFFRACTION100
3.5371-4.45560.15941460.14452779X-RAY DIFFRACTION100
4.4556-41.93110.18771530.17292895X-RAY DIFFRACTION99

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