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- PDB-5ouc: Crystal Structure of the Protein-Kinase A catalytic subunit from ... -

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Basic information

Entry
Database: PDB / ID: 5ouc
TitleCrystal Structure of the Protein-Kinase A catalytic subunit from Criteculus Griseus in complex with compounds RKp191 and RKp190
Components(cAMP-dependent protein kinase ...Protein kinase A) x 2
KeywordsTRANSFERASE / Complex / peptidic ligand
Function / homology
Function and homology information


regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity ...regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / axoneme / plasma membrane raft / mesoderm formation / sperm flagellum / negative regulation of smoothened signaling pathway / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / protein kinase A signaling / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / positive regulation of protein export from nucleus / acrosomal vesicle / neural tube closure / cellular response to glucose stimulus / 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 / dendritic spine / regulation of cell cycle / nuclear speck / protein domain specific binding / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / magnesium ion binding / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-AO8 / beta-D-ribopyranose / cAMP-dependent protein kinase inhibitor alpha / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsMueller, J.M. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Loewe-Corporation Germany
CitationJournal: To be published
Title: Crystal Structure of the Protein-Kinase A catalytic subunit from Criteculus Griseus in complex with compounds RKp191 and RKp190
Authors: Mueller, J.M. / Kirschner, R. / Heine, A. / Geyer, A. / Klebe, G.
History
DepositionAug 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
E: cAMP-dependent protein kinase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7545
Polymers43,1832
Non-polymers5713
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-7 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.585, 73.399, 108.357
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 AE

#1: Protein cAMP-dependent protein kinase catalytic subunit alpha / CAMP-dependent pathway / 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) / Tissue: Ovary / Gene: PRKACA / Organ: Ovary
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide cAMP-dependent protein kinase inhibitor / CAMP-dependent pathway


Mass: 1989.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PKI 5-22 with A17RBS mutation. / Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: G3HK48*PLUS

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Sugars , 1 types, 1 molecules

#4: Sugar ChemComp-RIP / beta-D-ribopyranose / Ribose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribopyranoseCOMMON NAMEGMML 1.0
b-D-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 240 molecules

#3: Chemical ChemComp-AO8 / [2-[[2-(isoquinolin-5-ylsulfonylamino)ethylamino]methyl]phenyl]boronic acid


Mass: 385.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20BN3O4S
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density meas: 57.66 Mg/m3 / Density % sol: 54.4 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 100 mM Mes-Bis-Tris, 75 mM lithium chloride, 1 mM DTT, 0.1 mM sodium EDTA, 0.25 mM Mega 8, 0.7 mM peptidic ligand, 5 mM RKp190, 20 % v/v methanol/water in reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.886 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 1.46→45.788 Å / Num. obs: 81889 / % possible obs: 99.8 % / Redundancy: 7.35 % / CC1/2: 0.998 / Rsym value: 0.057 / Net I/σ(I): 17.5
Reflection shellResolution: 1.46→1.55 Å / Redundancy: 7.18 % / Mean I/σ(I) obs: 2.94 / Num. unique obs: 13028 / CC1/2: 0.909 / Rsym value: 0.503 / % possible all: 99.3

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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 / Resolution: 1.46→45.788 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.18
RfactorNum. reflection% reflectionSelection details
Rfree0.1749 4095 5 %Random selection
Rwork0.1499 ---
obs0.1512 81887 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.46→45.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 32 238 3188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073055
X-RAY DIFFRACTIONf_angle_d0.8814149
X-RAY DIFFRACTIONf_dihedral_angle_d19.2511108
X-RAY DIFFRACTIONf_chiral_restr0.07442
X-RAY DIFFRACTIONf_plane_restr0.006552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4585-1.47570.22141370.1822603X-RAY DIFFRACTION97
1.4757-1.49370.21771400.16522660X-RAY DIFFRACTION100
1.4937-1.51260.231380.15322617X-RAY DIFFRACTION100
1.5126-1.53250.20171400.14422663X-RAY DIFFRACTION100
1.5325-1.55350.18291400.14542656X-RAY DIFFRACTION100
1.5535-1.57570.19091400.13542665X-RAY DIFFRACTION100
1.5757-1.59920.16731400.13782652X-RAY DIFFRACTION100
1.5992-1.62420.16821400.12582658X-RAY DIFFRACTION100
1.6242-1.65080.14491390.12052648X-RAY DIFFRACTION100
1.6508-1.67930.14261400.11652669X-RAY DIFFRACTION100
1.6793-1.70980.16011410.11912672X-RAY DIFFRACTION100
1.7098-1.74270.17211390.11412647X-RAY DIFFRACTION100
1.7427-1.77830.14181410.11062674X-RAY DIFFRACTION100
1.7783-1.8170.14481400.11562652X-RAY DIFFRACTION100
1.817-1.85920.14721390.11852652X-RAY DIFFRACTION100
1.8592-1.90570.16991410.12462677X-RAY DIFFRACTION100
1.9057-1.95730.16721410.13322681X-RAY DIFFRACTION100
1.9573-2.01490.14481410.13152665X-RAY DIFFRACTION100
2.0149-2.07990.16761410.14062691X-RAY DIFFRACTION100
2.0799-2.15420.16181410.14262670X-RAY DIFFRACTION100
2.1542-2.24050.14941410.13862685X-RAY DIFFRACTION100
2.2405-2.34240.1721420.14022703X-RAY DIFFRACTION100
2.3424-2.46590.15451420.14452700X-RAY DIFFRACTION100
2.4659-2.62040.15571430.14542702X-RAY DIFFRACTION100
2.6204-2.82270.20451420.16382702X-RAY DIFFRACTION100
2.8227-3.10670.18441430.16342716X-RAY DIFFRACTION100
3.1067-3.55610.19431440.17052736X-RAY DIFFRACTION100
3.5561-4.47970.17681460.15092783X-RAY DIFFRACTION100
4.4797-45.81060.18791530.1712893X-RAY DIFFRACTION100

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