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- PDB-5n3a: cAMP-dependent Protein Kinase A from Cricetulus griseus in comple... -

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Basic information

Entry
Database: PDB / ID: 5n3a
TitlecAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule 4-methyl-5-(1-methylimidazol-2-yl)-1,3-thiazol-2-amine
Components
  • cAMP dependent protein kinase inhibitor alpha-like protein
  • cAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / fragment / complex / serine threonine kinase / cAMP / kinase / PKA
Function / homology
Function and homology information


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 / regulation of osteoblast differentiation / cellular response to cold ...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 / 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 / intracellular potassium ion homeostasis / mesoderm formation / plasma membrane raft / axoneme / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / 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 / 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
Chem-46P / 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: 1.404 Å
AuthorsSiefker, C. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: A crystallographic fragment study with cAMP-dependent protein kinase A
Authors: Siefker, C. / 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 1.2Jan 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 1.3Oct 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)43,6566
Polymers43,1872
Non-polymers4694
Water4,450247
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-10 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.326, 72.411, 108.434
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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Protein / Protein/peptide , 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 alpha-like protein


Mass: 1993.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: G3HK48*PLUS

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Non-polymers , 4 types, 251 molecules

#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#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-46P / 4-methyl-5-(1-methyl-1H-imidazol-2-yl)-1,3-thiazol-2-amine


Mass: 194.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N4S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.82 Å3/Da / Density % sol: 56 %
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
RadiationMonochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 90107 / % possible obs: 99.9 % / Redundancy: 6.62 % / CC1/2: 1 / Rrim(I) all: 0.033 / Net I/σ(I): 28.34
Reflection shellResolution: 1.4→1.49 Å / Redundancy: 6.42 % / Mean I/σ(I) obs: 3.37 / Num. unique obs: 14385 / CC1/2: 0.89 / Rrim(I) all: 0.522 / % possible all: 99.8

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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: 1.404→39.71 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.7
RfactorNum. reflection% reflection
Rfree0.184 4504 5 %
Rwork0.1612 --
obs0.1623 90098 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.404→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2891 0 26 247 3164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073156
X-RAY DIFFRACTIONf_angle_d0.9074296
X-RAY DIFFRACTIONf_dihedral_angle_d19.2651150
X-RAY DIFFRACTIONf_chiral_restr0.079454
X-RAY DIFFRACTIONf_plane_restr0.006562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4045-1.42040.25241490.22482822X-RAY DIFFRACTION99
1.4204-1.43710.26421470.20662788X-RAY DIFFRACTION100
1.4371-1.45470.19091490.18242850X-RAY DIFFRACTION100
1.4547-1.47310.21731470.16992803X-RAY DIFFRACTION100
1.4731-1.49250.18561480.162814X-RAY DIFFRACTION100
1.4925-1.51290.18521480.15292802X-RAY DIFFRACTION100
1.5129-1.53450.17991510.15372868X-RAY DIFFRACTION100
1.5345-1.55740.20291460.15222784X-RAY DIFFRACTION100
1.5574-1.58180.18641510.14842855X-RAY DIFFRACTION100
1.5818-1.60770.16991480.14292821X-RAY DIFFRACTION100
1.6077-1.63540.18791490.13972822X-RAY DIFFRACTION100
1.6354-1.66520.17651490.13982845X-RAY DIFFRACTION100
1.6652-1.69720.18191490.13812821X-RAY DIFFRACTION100
1.6972-1.73180.15971490.13432831X-RAY DIFFRACTION100
1.7318-1.76950.17351490.13742834X-RAY DIFFRACTION100
1.7695-1.81070.20451510.14422863X-RAY DIFFRACTION100
1.8107-1.85590.19411490.14532835X-RAY DIFFRACTION100
1.8559-1.90610.19161490.15062833X-RAY DIFFRACTION100
1.9061-1.96220.20921490.15822835X-RAY DIFFRACTION100
1.9622-2.02550.17661500.15482845X-RAY DIFFRACTION100
2.0255-2.09790.17421500.15492849X-RAY DIFFRACTION100
2.0979-2.18190.17451500.15262862X-RAY DIFFRACTION100
2.1819-2.28120.15571500.14832852X-RAY DIFFRACTION100
2.2812-2.40150.16591520.1542875X-RAY DIFFRACTION100
2.4015-2.55190.16481510.16622866X-RAY DIFFRACTION100
2.5519-2.74890.19481520.17652899X-RAY DIFFRACTION100
2.7489-3.02540.18651530.17452893X-RAY DIFFRACTION100
3.0254-3.4630.19221530.17392921X-RAY DIFFRACTION100
3.463-4.36220.1791550.15482931X-RAY DIFFRACTION100
4.3622-39.72630.19091610.17283075X-RAY DIFFRACTION99

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