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- PDB-7ssb: Co-structure of PKG1 regulatory domain with compound 33 -

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Basic information

Entry
Database: PDB / ID: 7ssb
TitleCo-structure of PKG1 regulatory domain with compound 33
ComponentscGMP-dependent protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / binding sites / cyclic AMP / cyclic GMP / cyclic GMP-dependent / protein kinase type II / signaling protein / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of glutamate secretion / negative regulation of inositol phosphate biosynthetic process / 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 platelet aggregation / positive regulation of circadian rhythm / relaxation of vascular associated smooth muscle ...negative regulation of glutamate secretion / negative regulation of inositol phosphate biosynthetic process / 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 platelet aggregation / positive regulation of circadian rhythm / relaxation of vascular associated smooth muscle / Rap1 signalling / regulation of GTPase activity / cGMP-mediated signaling / mitogen-activated protein kinase p38 binding / spermatid development / cGMP effects / negative regulation of vascular associated smooth muscle cell migration / negative regulation of vascular associated smooth muscle cell proliferation / dendrite development / cGMP binding / forebrain development / calcium channel regulator activity / cerebellum development / acrosomal vesicle / sarcolemma / neuron migration / actin cytoskeleton organization / positive regulation of cytosolic calcium ion concentration / Ca2+ pathway / 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 / 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
Chem-B4I / cGMP-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFischmann, T.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Optimization and Mechanistic Investigations of Novel Allosteric Activators of PKG1 alpha.
Authors: Mak, V.W. / Patel, A.M. / Yen, R. / Hanisak, J. / Lim, Y.H. / Bao, J. / Zheng, R. / Seganish, W.M. / Yu, Y. / Healy, D.R. / Ogawa, A. / Ren, Z. / Soriano, A. / Ermakov, G.P. / Beaumont, M. / ...Authors: Mak, V.W. / Patel, A.M. / Yen, R. / Hanisak, J. / Lim, Y.H. / Bao, J. / Zheng, R. / Seganish, W.M. / Yu, Y. / Healy, D.R. / Ogawa, A. / Ren, Z. / Soriano, A. / Ermakov, G.P. / Beaumont, M. / Metwally, E. / Cheng, A.C. / Verras, A. / Fischmann, T. / Zebisch, M. / Silvestre, H.L. / McEwan, P.A. / Barker, J. / Rearden, P. / Greshock, T.J.
History
DepositionNov 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)31,0122
Polymers30,4671
Non-polymers5451
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.394, 80.656, 63.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-10150-

HOH

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Components

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


Mass: 30466.855 Da / Num. of mol.: 1 / Mutation: R203S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKG1, PRKG1B, PRKGR1A, PRKGR1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q13976, cGMP-dependent protein kinase
#2: Chemical ChemComp-B4I / 4-({(2S,3S)-3-[(1S)-1-(3,5-dichlorophenyl)-2-hydroxyethoxy]-2-phenylpiperidin-1-yl}methyl)-3-nitrobenzoic acid


Mass: 545.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H26Cl2N2O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.18 Å3/Da
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris 8.5 20 % v/v Glycerol ethoxylate, 3 % v/v Polyethyleneimine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.4→28.2 Å / Num. obs: 27749 / % possible obs: 97 % / Redundancy: 2.7 % / Biso Wilson estimate: 8.7 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.101 / Rrim(I) all: 0.199 / Net I/σ(I): 4 / Num. measured all: 76078
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.4220.285274813510.710.240.3751.597.4
7.67-28.23.50.0985591580.9720.0590.1156.578.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5jax

5jax


Resolution: 1.4→28.2 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.884 / SU R Cruickshank DPI: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.072 / SU Rfree Blow DPI: 0.069 / SU Rfree Cruickshank DPI: 0.066
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1076 3.88 %RANDOM
Rwork0.21 ---
obs0.211 27741 96.5 %-
Displacement parametersBiso max: 71.99 Å2 / Biso mean: 13.74 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.396 Å20 Å20 Å2
2---7.6961 Å20 Å2
3---7.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.4→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 192 0 1158
Biso mean--20.89 --
Num. residues----123
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d469SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes324HARMONIC5
X-RAY DIFFRACTIONt_it2057HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion140SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2276SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2057HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3724HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion4.2
X-RAY DIFFRACTIONt_other_torsion12.76
LS refinement shellResolution: 1.4→1.45 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.232 98 3.42 %
Rwork0.2063 2770 -
all0.2071 2868 -
obs--96.16 %

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