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- PDB-6c0t: Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ia... -

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Basic information

Entry
Database: PDB / ID: 6c0t
TitleCrystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain bound with N46
ComponentscGMP-dependent protein kinase 1
Keywordstransferase/transferase inhibitor / Serine/threonine protein kinases (EC 2.7.11.12) / TRANSFERASE / transferase-transferase inhibitor complex
Function / homology
Function and homology information


negative regulation of inositol phosphate biosynthetic process / negative regulation of glutamate secretion / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / collateral sprouting / negative regulation of vascular associated smooth muscle cell migration / negative regulation of platelet aggregation / relaxation of vascular associated smooth muscle ...negative regulation of inositol phosphate biosynthetic process / negative regulation of glutamate secretion / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / collateral sprouting / negative regulation of vascular associated smooth muscle cell migration / negative regulation of platelet aggregation / relaxation of vascular associated smooth muscle / positive regulation of circadian rhythm / Rap1 signalling / mitogen-activated protein kinase p38 binding / regulation of GTPase activity / cGMP-mediated signaling / dendrite development / spermatid development / cGMP effects / negative regulation of vascular associated smooth muscle cell proliferation / calcium channel regulator activity / cGMP binding / forebrain development / cerebellum development / acrosomal vesicle / neuron migration / sarcolemma / Ca2+ pathway / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / protein kinase activity / protein phosphorylation / protein serine kinase activity / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / 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-EE4 / TRIETHYLENE GLYCOL / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsQin, L. / Sankaran, B. / Kim, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM090161-08 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for selective inhibition of human PKG I alpha by the balanol-like compound N46.
Authors: Qin, L. / Sankaran, B. / Aminzai, S. / Casteel, D.E. / Kim, C.
History
DepositionJan 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cGMP-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2624
Polymers39,4741
Non-polymers7883
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.730, 85.730, 50.664
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein cGMP-dependent protein kinase 1 / cGK1 / cGMP-dependent protein kinase I / cGKI


Mass: 39473.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N46 / Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG1, PRKG1B, PRKGR1A, PRKGR1B / Plasmid: pBlueBacHis2A / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13976, cGMP-dependent protein kinase
#2: Chemical ChemComp-EE4 / N-[(3R,4R)-4-{[4-(2-fluoro-3-methoxy-6-propoxybenzene-1-carbonyl)benzene-1-carbonyl]amino}pyrrolidin-3-yl]-1H-indazole-5-carboxamide


Mass: 559.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H30FN5O5
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24%w/v PEG1500, 20%v/v glycerol, 3% w/v Trimethylamine N-oxide dihydrate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→43.62 Å / Num. obs: 25870 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.1
Reflection shellResolution: 1.98→2.03 Å / Rmerge(I) obs: 0.904 / CC1/2: 0.912

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BG2

6bg2


Resolution: 1.98→42.865 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 1992 7.72 %
Rwork0.2072 --
obs0.2101 25804 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→42.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 55 98 2759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072730
X-RAY DIFFRACTIONf_angle_d0.7783701
X-RAY DIFFRACTIONf_dihedral_angle_d17.947970
X-RAY DIFFRACTIONf_chiral_restr0.048395
X-RAY DIFFRACTIONf_plane_restr0.005473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.02950.33741430.33841694X-RAY DIFFRACTION99
2.0295-2.08440.31721420.30381683X-RAY DIFFRACTION100
2.0844-2.14570.30991440.29221683X-RAY DIFFRACTION100
2.1457-2.2150.30571330.27451685X-RAY DIFFRACTION100
2.215-2.29410.28021410.26711685X-RAY DIFFRACTION100
2.2941-2.3860.31931470.26041715X-RAY DIFFRACTION100
2.386-2.49460.29091420.26641668X-RAY DIFFRACTION100
2.4946-2.62610.31761440.26081703X-RAY DIFFRACTION100
2.6261-2.79060.3111370.25211694X-RAY DIFFRACTION100
2.7906-3.0060.31191400.24261693X-RAY DIFFRACTION100
3.006-3.30840.24061450.23031719X-RAY DIFFRACTION100
3.3084-3.78690.22611430.19081699X-RAY DIFFRACTION100
3.7869-4.770.23021460.15571728X-RAY DIFFRACTION100
4.77-42.8750.17821450.17141763X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -22.6016 Å / Origin y: 18.2327 Å / Origin z: 6.4865 Å
111213212223313233
T0.4136 Å20.0075 Å2-0.0878 Å2-0.304 Å2-0.0302 Å2--0.2884 Å2
L3.0154 °20.6381 °20.3903 °2-2.3394 °2-0.771 °2--2.516 °2
S-0.0476 Å °-0.1747 Å °0.1589 Å °-0.0024 Å °0.0304 Å °0.2465 Å °-0.0077 Å °0.2584 Å °0.0173 Å °
Refinement TLS groupSelection details: all

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