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- PDB-5o2b: Crystal structure of WNK3 kinase domain in a diphosphorylated sta... -

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Basic information

Entry
Database: PDB / ID: 5o2b
TitleCrystal structure of WNK3 kinase domain in a diphosphorylated state and in a complex with the inhibitor PP-121
ComponentsSerine/threonine-protein kinase WNK3
KeywordsSTRUCTURAL GENOMICS / WNK3 / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of sodium ion transmembrane transporter activity / positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / monoatomic ion homeostasis / non-membrane-bounded organelle assembly / regulation of calcium ion import / osmosensory signaling pathway / positive regulation of sodium ion transport / cellular hyperosmotic response / positive regulation of calcium ion transport ...positive regulation of sodium ion transmembrane transporter activity / positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / monoatomic ion homeostasis / non-membrane-bounded organelle assembly / regulation of calcium ion import / osmosensory signaling pathway / positive regulation of sodium ion transport / cellular hyperosmotic response / positive regulation of calcium ion transport / regulation of monoatomic cation transmembrane transport / cell volume homeostasis / negative regulation of protein localization to plasma membrane / maintenance of blood-brain barrier / bicellular tight junction / molecular condensate scaffold activity / positive regulation of peptidyl-threonine phosphorylation / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / adherens junction / peptidyl-threonine phosphorylation / Stimuli-sensing channels / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / ATP binding / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / 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 ...Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-KS1 / Serine/threonine-protein kinase WNK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.038 Å
AuthorsPinkas, D.M. / Bufton, J.C. / Newman, J.A. / Borkowska, O. / Chalk, R. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Pinkas, D.M. / Bufton, J.C. / Newman, J.A. / Borkowska, O. / Chalk, R. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of WNK3 kinase domain in a diphosphorylated state and in a complex with the inhibitor PP-121
Authors: Pinkas, D.M. / Daubner, G.M. / Bufton, J.C. / Bartual, S.G. / Sanvitale, C.E. / Alessi, D.R. / Bullock, A.
History
DepositionMay 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 19, 2017Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / entity / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _entity.pdbx_description / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase WNK3
B: Serine/threonine-protein kinase WNK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9715
Polymers65,3102
Non-polymers6623
Water4,540252
1
A: Serine/threonine-protein kinase WNK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9973
Polymers32,6551
Non-polymers3422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase WNK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9742
Polymers32,6551
Non-polymers3191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.160, 71.253, 67.800
Angle α, β, γ (deg.)90.00, 103.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase WNK3 / Protein kinase lysine-deficient 3 / Protein kinase with no lysine 3


Mass: 32654.871 Da / Num. of mol.: 2 / Fragment: UNP residues 132-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WNK3, KIAA1566, PRKWNK3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9BYP7, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-KS1 / 1-cyclopentyl-3-(1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 319.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17N7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 0.2M magnesium chloride, 0.1M bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.038→71.253 Å / Num. obs: 35449 / % possible obs: 99.4 % / Redundancy: 3.4 % / Net I/σ(I): 12.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.038→50.05 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.91
RfactorNum. reflection% reflection
Rfree0.2401 1803 5.09 %
Rwork0.199 --
obs0.2012 35425 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.038→50.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4023 0 49 252 4324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084167
X-RAY DIFFRACTIONf_angle_d0.9185648
X-RAY DIFFRACTIONf_dihedral_angle_d15.1762484
X-RAY DIFFRACTIONf_chiral_restr0.058643
X-RAY DIFFRACTIONf_plane_restr0.007704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0378-2.09290.30391560.24832569X-RAY DIFFRACTION99
2.0929-2.15450.30541270.23952558X-RAY DIFFRACTION99
2.1545-2.22410.36111460.2392569X-RAY DIFFRACTION99
2.2241-2.30350.28371300.21752557X-RAY DIFFRACTION99
2.3035-2.39580.25581450.21072584X-RAY DIFFRACTION100
2.3958-2.50480.29881300.22342602X-RAY DIFFRACTION100
2.5048-2.63690.2711220.22022590X-RAY DIFFRACTION100
2.6369-2.8020.30781560.21882590X-RAY DIFFRACTION100
2.802-3.01840.2131380.20542573X-RAY DIFFRACTION100
3.0184-3.32210.26771470.20242581X-RAY DIFFRACTION99
3.3221-3.80260.18711320.18212606X-RAY DIFFRACTION99
3.8026-4.79030.19561270.16032620X-RAY DIFFRACTION99
4.7903-50.06480.22151470.20262623X-RAY DIFFRACTION98

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