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

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Basic information

Entry
Database: PDB / ID: 6yps
TitleCrystal structure of the cAMP-dependent protein kinase A in complex with 4-hydroxybenzamidine
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 / regulation of osteoblast differentiation / cellular response to cold / 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 / 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 / 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 / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol
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
4-oxidanylbenzenecarboximidamide / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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
DepositionApr 16, 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
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)41,4083
Polymers41,1941
Non-polymers2142
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint4 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.736, 71.316, 97.495
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: 41193.746 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-P72 / 4-oxidanylbenzenecarboximidamide


Mass: 136.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.348→48.75 Å / Num. obs: 78185 / % possible obs: 97.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.042 / Net I/σ(I): 22.58
Reflection shellResolution: 1.35→1.43 Å / Mean I/σ(I) obs: 3.53 / Num. unique obs: 12184 / Rsym value: 0.529

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→48.75 Å / SU ML: 0.0997 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.915
RfactorNum. reflection% reflection
Rfree0.157 3910 5 %
Rwork0.1441 --
obs0.1448 78180 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.16 Å2
Refinement stepCycle: LAST / Resolution: 1.35→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 14 234 2958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762979
X-RAY DIFFRACTIONf_angle_d0.93384061
X-RAY DIFFRACTIONf_chiral_restr0.08428
X-RAY DIFFRACTIONf_plane_restr0.0072535
X-RAY DIFFRACTIONf_dihedral_angle_d20.31191088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.360.24241310.21742473X-RAY DIFFRACTION92.31
1.36-1.380.22221350.17272584X-RAY DIFFRACTION95.74
1.38-1.40.19171370.14682592X-RAY DIFFRACTION95.86
1.4-1.420.15711340.13522548X-RAY DIFFRACTION95.99
1.42-1.440.15831360.12712576X-RAY DIFFRACTION96
1.44-1.460.17641360.122598X-RAY DIFFRACTION96.23
1.46-1.480.14721370.11232586X-RAY DIFFRACTION96.42
1.48-1.510.12561360.10992600X-RAY DIFFRACTION96.64
1.51-1.530.13631380.10652617X-RAY DIFFRACTION96.8
1.53-1.560.14721380.10832614X-RAY DIFFRACTION96.83
1.56-1.590.15121370.11192600X-RAY DIFFRACTION96.92
1.59-1.620.15961400.10962672X-RAY DIFFRACTION97.13
1.62-1.660.14291380.11472618X-RAY DIFFRACTION97.52
1.66-1.70.16391390.1162632X-RAY DIFFRACTION97.81
1.7-1.740.15861380.11822627X-RAY DIFFRACTION97.46
1.74-1.790.15941400.12392656X-RAY DIFFRACTION97.83
1.79-1.840.18051400.12422662X-RAY DIFFRACTION97.94
1.84-1.90.16221400.12612659X-RAY DIFFRACTION98.24
1.9-1.970.14311400.12522666X-RAY DIFFRACTION98.39
1.97-2.050.12881420.12472690X-RAY DIFFRACTION98.44
2.05-2.140.1311400.12862679X-RAY DIFFRACTION98.64
2.14-2.250.15591430.13022712X-RAY DIFFRACTION98.65
2.25-2.390.15891420.13422689X-RAY DIFFRACTION98.78
2.39-2.580.14791440.14842736X-RAY DIFFRACTION99.17
2.58-2.840.16251440.15372732X-RAY DIFFRACTION99.1
2.84-3.250.17421450.15982762X-RAY DIFFRACTION99.05
3.25-4.090.14321460.15132770X-RAY DIFFRACTION99.15
4.09-48.750.16911540.17712920X-RAY DIFFRACTION99.16

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