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- PDB-6i2c: Crystal Structure of the Protein-Kinase A catalytic subunit from ... -

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Basic information

Entry
Database: PDB / ID: 6i2c
TitleCrystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus Griseus in complex with compounds RKp182 and Fasudil
Components
  • UPF0418 protein FAM164A
  • cAMP-dependent protein kinase catalytic subunit alpha
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 / regulation of osteoblast differentiation / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / cAMP-dependent protein kinase activity / sperm capacitation ...regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / regulation of osteoblast differentiation / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / cAMP-dependent protein kinase activity / sperm capacitation / cAMP-dependent protein kinase complex / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / AMP-activated protein kinase activity / postsynaptic modulation of chemical synaptic transmission / protein kinase A regulatory subunit binding / plasma membrane raft / axoneme / 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 / cellular response to glucagon stimulus / protein kinase A signaling / protein serine/threonine/tyrosine kinase activity / protein export from nucleus / acrosomal vesicle / positive regulation of protein export from nucleus / 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 / 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
5-(1,4-DIAZEPAN-1-SULFONYL)ISOQUINOLINE / 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: 1.82 Å
AuthorsMueller, J.M. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other government 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
DepositionNov 1, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionMay 15, 2019ID: 6ERS
Revision 1.0May 15, 2019Provider: 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.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: UPF0418 protein FAM164A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6394
Polymers43,1982
Non-polymers4412
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint3 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.338, 73.088, 77.183
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 / 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 UPF0418 protein FAM164A


Mass: 2004.188 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: PKI 5-22 with G17RBS mutation. A ribose has been covalently attached to a serine in the peptide.
Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: G3HK48
#3: Chemical ChemComp-M77 / 5-(1,4-DIAZEPAN-1-SULFONYL)ISOQUINOLINE / Fasudil / (5-ISOQUINOLINESULFONYL)HOMOPIPERAZINE


Mass: 291.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N3O2S / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#4: Sugar ChemComp-RIP / beta-D-ribopyranose / beta-D-ribose / D-ribose / ribose / RIBOSE(PYRANOSE FORM)


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.74 %
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 Fasudil, 16% v/v methanol/water in reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.82→34.126 Å / Num. obs: 35803 / % possible obs: 99.8 % / Redundancy: 5.49 % / CC1/2: 0.998 / Rsym value: 0.082 / Net I/σ(I): 13.29
Reflection shellResolution: 1.82→1.93 Å / Redundancy: 5.51 % / Mean I/σ(I) obs: 2.91 / Num. unique obs: 5705 / CC1/2: 0.841 / Rsym value: 0.507 / % possible all: 99.5

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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: 1.82→34.126 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.84
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 1790 5 %Random selection
Rwork0.1851 ---
obs0.1869 35796 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.82→34.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 26 141 2979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012922
X-RAY DIFFRACTIONf_angle_d0.9963970
X-RAY DIFFRACTIONf_dihedral_angle_d14.7721718
X-RAY DIFFRACTIONf_chiral_restr0.064427
X-RAY DIFFRACTIONf_plane_restr0.007521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8194-1.86850.27121360.22532571X-RAY DIFFRACTION99
1.8685-1.92350.23561360.20972582X-RAY DIFFRACTION100
1.9235-1.98560.29281350.21872564X-RAY DIFFRACTION100
1.9856-2.05660.23591360.20622582X-RAY DIFFRACTION100
2.0566-2.13890.23551360.2052586X-RAY DIFFRACTION100
2.1389-2.23620.22761360.18392600X-RAY DIFFRACTION100
2.2362-2.35410.23261370.18192595X-RAY DIFFRACTION100
2.3541-2.50150.22531370.17932597X-RAY DIFFRACTION100
2.5015-2.69460.22371370.18912617X-RAY DIFFRACTION100
2.6946-2.96560.24891390.2022639X-RAY DIFFRACTION100
2.9656-3.39440.23491380.19862615X-RAY DIFFRACTION100
3.3944-4.27530.20761410.16562687X-RAY DIFFRACTION100
4.2753-34.13240.17691460.16432771X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6516-0.3206-0.06580.2586-0.10670.5719-0.07870.1536-0.0569-0.1031-0.0073-0.0415-0.13420.14440.00010.1493-0.04350.02290.21760.00710.187617.512519.62963.6378
20.671-0.0786-0.13490.6243-0.01120.4663-0.03340.0573-0.1050.023-0.01480.0564-0.02620.04-0.00160.0840.0017-0.00920.1282-0.01520.121311.230316.702810.8446
31.42170.2424-0.140.9997-0.08620.41150.0367-0.24760.0440.1773-0.02410.1784-0.05470.0810.00520.1810.00770.04030.1272-0.01590.13155.614519.37527.3435
40.31380.0255-0.36690.70820.58260.9547-0.0394-0.0022-0.1044-0.03270.03220.1320.1124-0.0321-0.00020.1091-0.05150.00690.18430.03560.205612.330512.92387.3499
50.02910.00190.02630.01250.01320.03430.0422-0.2192-0.29790.02010.07790.1777-0.11310.0861-0.00010.20620.00670.06240.18780.04160.3239-6.7552.883328.8351
60.0068-0.011-0.01240.01840.01690.02580.00180.0951-0.1864-0.4307-0.03060.2326-0.1894-0.0737-0.00030.23160.01920.00340.14570.00330.2997-3.862911.527117.5042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 67 )
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 160 )
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 297 )
4X-RAY DIFFRACTION4chain 'A' and (resid 298 through 350 )
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 19 )
6X-RAY DIFFRACTION6chain 'B' and (resid 20 through 28 )

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