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- PDB-6snx: Crystal structure of cAMP-dependent protein kinase A (CHO PKA) in... -

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Basic information

Entry
Database: PDB / ID: 6snx
TitleCrystal structure of cAMP-dependent protein kinase A (CHO PKA) in complex with benzamide
ComponentscAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / phosphotransferase / signalling pathways / glycogen metabolism / serine/threonine kinase
Function / homology
Function and homology information


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 / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation ...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 / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / plasma membrane raft / axoneme / 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 / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / neuromuscular junction / 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 / centrosome / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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. ...cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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
Similarity search - Domain/homology
BENZAMIDE / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsOebbeke, M. / Siefker, C. / 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
DepositionAug 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 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 1.2Dec 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
Revision 1.3Jan 24, 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3563
Polymers41,1141
Non-polymers2422
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-7 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.738, 71.261, 97.135
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 / 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) (bacteria) / References: UniProt: P25321, cAMP-dependent protein kinase
#2: Chemical ChemComp-UNU / BENZAMIDE


Mass: 121.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 100 mM MES-BIS-Tris-Buffer, 1 mM dithiothreitol, 0.1 mM sodium EDTA, 75 mM LiCl, 0.03 Mega 8 and 23 % methanol (v/v) 0.003 mL drop volume, 0.5 mL reservoir volume

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.8655 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8655 Å / Relative weight: 1
ReflectionResolution: 1.4→45.66 Å / Num. obs: 70483 / % possible obs: 98.2 % / Redundancy: 4.5 % / Rsym value: 0.096 / Net I/σ(I): 8.5
Reflection shellResolution: 1.4→1.48 Å / Num. unique obs: 11148 / Rsym value: 0.045

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Processing

Software
NameVersionClassification
PHASERphasing
Coot0.8.9model building
PDB-REDOrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F14

6f14


Resolution: 1.4→45.66 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1734 3519 5 %
Rwork0.1422 --
obs-70374 98.2 %
Displacement parametersBiso mean: 18.77 Å2
Refinement stepCycle: LAST / Resolution: 1.4→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2740 0 18 293 3051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723037
X-RAY DIFFRACTIONf_angle_d0.94344144
X-RAY DIFFRACTIONf_chiral_restr0.0805435
X-RAY DIFFRACTIONf_plane_restr0.0062555
X-RAY DIFFRACTIONf_dihedral_angle_d21.89881120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.21710.19782637X-RAY DIFFRACTION99.39
1.42-1.440.20491400.16252667X-RAY DIFFRACTION99.43
1.44-1.460.20861400.14932658X-RAY DIFFRACTION99.4
1.46-1.480.17891390.14422641X-RAY DIFFRACTION98.41
1.48-1.510.1871370.1422608X-RAY DIFFRACTION97.37
1.51-1.530.19981380.13812620X-RAY DIFFRACTION97.32
1.53-1.560.1761350.13532551X-RAY DIFFRACTION94.68
1.56-1.590.15611380.12992633X-RAY DIFFRACTION97.92
1.59-1.620.16311410.12212679X-RAY DIFFRACTION99.23
1.62-1.660.17661400.12272659X-RAY DIFFRACTION98.94
1.66-1.70.1921410.12532672X-RAY DIFFRACTION99.29
1.7-1.740.18771400.12072658X-RAY DIFFRACTION98.8
1.74-1.790.16061400.12152662X-RAY DIFFRACTION98.66
1.79-1.840.15841410.1212676X-RAY DIFFRACTION99.05
1.84-1.90.15241400.1282676X-RAY DIFFRACTION98.6
1.9-1.970.17631400.13312660X-RAY DIFFRACTION98.7
1.97-2.050.1691410.13532666X-RAY DIFFRACTION98.25
2.05-2.140.14891400.13412673X-RAY DIFFRACTION98.49
2.14-2.250.15551430.13142710X-RAY DIFFRACTION98.99
2.25-2.390.15981420.13352707X-RAY DIFFRACTION99.69
2.39-2.580.17931440.14082723X-RAY DIFFRACTION99.31
2.58-2.840.17451370.14962611X-RAY DIFFRACTION94.96
2.84-3.250.17781440.14732726X-RAY DIFFRACTION98.19
3.25-4.090.17491460.14632781X-RAY DIFFRACTION99.73
4.09-41.890.18241530.16482895X-RAY DIFFRACTION98.64

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