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- PDB-5o5m: Crystal Structure of the Protein-Kinase A catalytic subunit from ... -

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Basic information

Entry
Database: PDB / ID: 5o5m
TitleCrystal Structure of the Protein-Kinase A catalytic subunit from Criteculus Griseus in complex with compounds RKp120 and RKp117
Components
  • RKp120
  • cAMP-dependent protein kinase catalytic subunit alphaCAMP-dependent pathway
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 / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / 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 / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / cellular response to heat / manganese ion binding / dendritic spine / regulation of cell cycle / nuclear speck / protein domain specific binding / phosphorylation / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / 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-9LQ / 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: 1.583 Å
AuthorsMueller, J.M. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Loewe-Corporation Germany
CitationJournal: Acs Omega / Year: 2019
Title: Conceptional Design of Self-Assembling Bisubstrate-like Inhibitors of Protein Kinase A Resulting in a Boronic Acid Glutamate Linkage
Authors: Mueller, J.M. / Kirschner, R. / Geyer, A. / Klebe, G.
History
DepositionJun 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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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
C: RKp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6014
Polymers43,1402
Non-polymers4612
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-11 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.982, 72.633, 76.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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 RKp120


Mass: 1946.152 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: cAMP-dependent protein kinase inhibitor with N15RBS mutation. The ribose attached to the serine is disordered and not visible.
Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: G3HK48*PLUS
#3: Chemical ChemComp-9LQ / [2-[(4-isoquinolin-5-ylsulfonyl-1,4-diazepan-1-yl)methyl]phenyl]boronic acid


Mass: 425.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24BN3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 5 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 RKp117, 15 % v/v methanol/water in reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.583→50 Å / Num. obs: 53352 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rsym value: 0.034 / Net I/σ(I): 26.99
Reflection shellResolution: 1.583→1.68 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.53 / Num. unique obs: 8345 / CC1/2: 0.895 / Rsym value: 0.492 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.583→41.918 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.44
RfactorNum. reflection% reflectionSelection details
Rfree0.1824 2668 5 %Random selection
Rwork0.148 ---
obs0.1497 53348 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.583→41.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 31 255 3126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083012
X-RAY DIFFRACTIONf_angle_d0.9324101
X-RAY DIFFRACTIONf_dihedral_angle_d14.0821790
X-RAY DIFFRACTIONf_chiral_restr0.054437
X-RAY DIFFRACTIONf_plane_restr0.006545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5794-1.60810.32261300.23762460X-RAY DIFFRACTION93
1.6081-1.63910.27551390.22645X-RAY DIFFRACTION100
1.6391-1.67250.25081380.16642635X-RAY DIFFRACTION100
1.6725-1.70890.21651390.14192630X-RAY DIFFRACTION100
1.7089-1.74870.17161400.12992661X-RAY DIFFRACTION100
1.7487-1.79240.23391390.12252637X-RAY DIFFRACTION100
1.7924-1.84090.17841380.12032635X-RAY DIFFRACTION100
1.8409-1.8950.19261400.12672657X-RAY DIFFRACTION100
1.895-1.95620.18721410.13392666X-RAY DIFFRACTION100
1.9562-2.02610.18111410.14042682X-RAY DIFFRACTION100
2.0261-2.10720.2041390.13682640X-RAY DIFFRACTION100
2.1072-2.20310.16841410.13242677X-RAY DIFFRACTION100
2.2031-2.31930.17181390.12652658X-RAY DIFFRACTION100
2.3193-2.46460.17531430.13092698X-RAY DIFFRACTION100
2.4646-2.65480.17211400.14172678X-RAY DIFFRACTION100
2.6548-2.92190.19491420.15512697X-RAY DIFFRACTION100
2.9219-3.34460.18831440.15932723X-RAY DIFFRACTION100
3.3446-4.21320.15241440.14652736X-RAY DIFFRACTION100
4.2132-41.93280.18361510.16442865X-RAY DIFFRACTION100

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