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- PDB-6z44: Crystal structure of the cAMP-dependent protein kinase A in compl... -

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Basic information

Entry
Database: PDB / ID: 6z44
TitleCrystal structure of the cAMP-dependent protein kinase A in complex with phenol
ComponentscAMP-dependent protein kinase catalytic subunit alphaCAMP-dependent pathway
KeywordsTRANSFERASE / phosphotransferase / signalling pathways / glycogen metabolism / serine/threonine kinase
Function / homology
Function and homology information


cAMP-dependent protein kinase / cellular response to parathyroid hormone stimulus / negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / cellular response to cold ...cAMP-dependent protein kinase / cellular response to parathyroid hormone stimulus / negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / cellular response to cold / ciliary base / sperm capacitation / sperm flagellum / regulation of osteoblast differentiation / protein kinase A regulatory subunit binding / axoneme / plasma membrane raft / mesoderm formation / protein export from nucleus / regulation of proteasomal protein catabolic process / acrosomal vesicle / positive regulation of protein export from nucleus / protein serine/threonine/tyrosine kinase activity / modulation of chemical synaptic transmission / neural tube closure / cellular response to glucose stimulus / neuromuscular junction / mRNA processing / cellular response to heat / peptidyl-threonine phosphorylation / manganese ion binding / dendritic spine / regulation of cell cycle / nuclear speck / peptidyl-serine phosphorylation / protein autophosphorylation / centrosome / protein domain specific binding / protein serine kinase activity / ubiquitin protein ligase binding / protein serine/threonine kinase activity / protein kinase binding / perinuclear region of cytoplasm / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase C-terminal domain profile. / AGC-kinase, C-terminal / Serine/Threonine protein kinases active-site signature. / Serine/threonine-protein kinase, active site / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase C-terminal domain profile. / AGC-kinase, C-terminal / Serine/Threonine protein kinases active-site signature. / Serine/threonine-protein kinase, active site / 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
Similarity search - Domain/homology
PHENOL / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsOebbeke, M. / Heine, A. / Klebe, G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
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
DepositionMay 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5606
Polymers41,1141
Non-polymers4475
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint13 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.775, 71.385, 97.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 41113.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: PRKACA / Production host: Escherichia coli BL21(DE3) (unknown) / References: UniProt: P25321, cAMP-dependent protein kinase
#2: Chemical ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0,2 mM PKA in 100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 mM Mega 8 and 23 % methanol (v/v) 0.003 mL drop volume, 0.5 mL reservoir volume Soaking: ...Details: 0,2 mM PKA in 100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.2 mM Mega 8 and 23 % methanol (v/v) 0.003 mL drop volume, 0.5 mL reservoir volume Soaking: 100mM phenol in buffer described above and 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.379→48.705 Å / Num. obs: 74984 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 15.85 Å2 / Rsym value: 0.042 / Net I/σ(I): 21.7
Reflection shellResolution: 1.38→1.46 Å / Mean I/σ(I) obs: 3.07 / Num. unique obs: 11843 / Rsym value: 0.497

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F14
Resolution: 1.38→20.12 Å / SU ML: 0.0995 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.2211
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1736 3748 5 %
Rwork0.1451 71207 -
obs0.1465 74955 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.12 Å2
Refinement stepCycle: LAST / Resolution: 1.38→20.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 27 256 2997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672926
X-RAY DIFFRACTIONf_angle_d0.93533976
X-RAY DIFFRACTIONf_chiral_restr0.0774416
X-RAY DIFFRACTIONf_plane_restr0.0067512
X-RAY DIFFRACTIONf_dihedral_angle_d22.59841066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.40.24011310.18952486X-RAY DIFFRACTION95.09
1.4-1.410.22811360.17312582X-RAY DIFFRACTION100
1.41-1.430.2371390.16492631X-RAY DIFFRACTION100
1.43-1.450.19821360.15642592X-RAY DIFFRACTION100
1.45-1.480.16491380.13912626X-RAY DIFFRACTION100
1.48-1.50.17611370.12912591X-RAY DIFFRACTION100
1.5-1.520.17921380.12592627X-RAY DIFFRACTION100
1.52-1.550.15691370.1182613X-RAY DIFFRACTION100
1.55-1.580.15531380.12542622X-RAY DIFFRACTION100
1.58-1.610.16851380.12142612X-RAY DIFFRACTION100
1.61-1.640.16511370.1182605X-RAY DIFFRACTION100
1.64-1.680.19521390.12032640X-RAY DIFFRACTION100
1.68-1.720.1251370.11862602X-RAY DIFFRACTION100
1.72-1.760.15431380.11782617X-RAY DIFFRACTION100
1.76-1.810.15811390.11992653X-RAY DIFFRACTION100
1.81-1.860.1731380.13012624X-RAY DIFFRACTION100
1.86-1.920.15851410.13432661X-RAY DIFFRACTION99.96
1.92-1.990.18141380.13712635X-RAY DIFFRACTION99.96
1.99-2.070.1791380.13452613X-RAY DIFFRACTION100
2.07-2.160.14971410.13472681X-RAY DIFFRACTION99.96
2.16-2.280.14411380.1332615X-RAY DIFFRACTION99.82
2.28-2.420.14561390.1362657X-RAY DIFFRACTION100
2.42-2.60.1691400.14832663X-RAY DIFFRACTION99.93
2.6-2.860.18461420.15512696X-RAY DIFFRACTION99.96
2.87-3.280.19341420.15892687X-RAY DIFFRACTION99.89
3.28-4.120.18091430.15142717X-RAY DIFFRACTION100
4.12-20.120.18291500.16652859X-RAY DIFFRACTION99.97

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