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- PDB-5drb: Crystal structure of WNK1 in complex with WNK463 -

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Basic information

Entry
Database: PDB / ID: 5drb
TitleCrystal structure of WNK1 in complex with WNK463
ComponentsSerine/threonine-protein kinase WNK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / inhibitor / complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / positive regulation of termination of RNA polymerase II transcription / monoatomic cation homeostasis / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / positive regulation of mitotic cytokinesis / monoatomic ion homeostasis / negative regulation of sodium ion transport ...negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / positive regulation of termination of RNA polymerase II transcription / monoatomic cation homeostasis / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / positive regulation of mitotic cytokinesis / monoatomic ion homeostasis / negative regulation of sodium ion transport / positive regulation of potassium ion import across plasma membrane / regulation of mRNA export from nucleus / regulation of sodium ion transmembrane transport / intracellular chloride ion homeostasis / negative regulation of heterotypic cell-cell adhesion / non-membrane-bounded organelle assembly / positive regulation of T cell chemotaxis / positive regulation of systemic arterial blood pressure / potassium channel inhibitor activity / potassium ion homeostasis / cellular hyperosmotic response / cellular response to chemokine / protein serine/threonine kinase inhibitor activity / negative regulation of leukocyte cell-cell adhesion / regulation of monoatomic cation transmembrane transport / cell volume homeostasis / negative regulation of protein localization to plasma membrane / intracellular non-membrane-bounded organelle / protein kinase activator activity / sodium ion transmembrane transport / GABA-ergic synapse / phosphatase binding / monoatomic ion transport / regulation of sodium ion transport / negative regulation of protein ubiquitination / cellular response to calcium ion / molecular condensate scaffold activity / negative regulation of autophagy / modulation of chemical synaptic transmission / mitotic spindle / regulation of blood pressure / positive regulation of canonical Wnt signaling pathway / positive regulation of angiogenesis / heart development / T cell receptor signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / signal transduction / protein-containing complex / ATP binding / membrane / nucleus / cytosol / 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-5FJ / Serine/threonine-protein kinase WNK1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsKohls, D. / Xie, X.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Small-molecule WNK inhibition regulates cardiovascular and renal function.
Authors: Yamada, K. / Park, H.M. / Rigel, D.F. / DiPetrillo, K. / Whalen, E.J. / Anisowicz, A. / Beil, M. / Berstler, J. / Brocklehurst, C.E. / Burdick, D.A. / Caplan, S.L. / Capparelli, M.P. / Chen, ...Authors: Yamada, K. / Park, H.M. / Rigel, D.F. / DiPetrillo, K. / Whalen, E.J. / Anisowicz, A. / Beil, M. / Berstler, J. / Brocklehurst, C.E. / Burdick, D.A. / Caplan, S.L. / Capparelli, M.P. / Chen, G. / Chen, W. / Dale, B. / Deng, L. / Fu, F. / Hamamatsu, N. / Harasaki, K. / Herr, T. / Hoffmann, P. / Hu, Q.Y. / Huang, W.J. / Idamakanti, N. / Imase, H. / Iwaki, Y. / Jain, M. / Jeyaseelan, J. / Kato, M. / Kaushik, V.K. / Kohls, D. / Kunjathoor, V. / LaSala, D. / Lee, J. / Liu, J. / Luo, Y. / Ma, F. / Mo, R. / Mowbray, S. / Mogi, M. / Ossola, F. / Pandey, P. / Patel, S.J. / Raghavan, S. / Salem, B. / Shanado, Y.H. / Trakshel, G.M. / Turner, G. / Wakai, H. / Wang, C. / Weldon, S. / Wielicki, J.B. / Xie, X. / Xu, L. / Yagi, Y.I. / Yasoshima, K. / Yin, J. / Yowe, D. / Zhang, J.H. / Zheng, G. / Monovich, L.
History
DepositionSep 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase WNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0022
Polymers33,5391
Non-polymers4631
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.642, 57.670, 65.532
Angle α, β, γ (deg.)90.00, 89.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase WNK1 / Protein kinase lysine-deficient 1 / Protein kinase with no lysine 1


Mass: 33538.551 Da / Num. of mol.: 1 / Fragment: UNP residues 194-483 / Mutation: S382A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Wnk1, Hsn2, Prkwnk1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9JIH7, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-5FJ / N-tert-butyl-1-(1-{5-[5-(trifluoromethyl)-1,3,4-oxadiazol-2-yl]pyridin-2-yl}piperidin-4-yl)-1H-imidazole-5-carboxamide


Mass: 463.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24F3N7O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8 / Details: 100 mM Tris, pH 8.0, 16% PEG550 MME, 4% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→65.53 Å / Num. obs: 34584 / % possible obs: 99.4 % / Redundancy: 3.3 % / Net I/σ(I): 21.8
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.2 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.65→65.53 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2405 1729 5 %
Rwork0.1969 --
obs0.1991 34577 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→65.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 33 254 2483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072292
X-RAY DIFFRACTIONf_angle_d1.1373090
X-RAY DIFFRACTIONf_dihedral_angle_d17.787873
X-RAY DIFFRACTIONf_chiral_restr0.082338
X-RAY DIFFRACTIONf_plane_restr0.004389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69860.31271410.28392693X-RAY DIFFRACTION98
1.6986-1.75340.29361440.26242732X-RAY DIFFRACTION100
1.7534-1.81610.29031440.24792732X-RAY DIFFRACTION100
1.8161-1.88880.27651420.23652709X-RAY DIFFRACTION100
1.8888-1.97470.29891450.24242737X-RAY DIFFRACTION100
1.9747-2.07890.27051440.22212741X-RAY DIFFRACTION100
2.0789-2.20910.26441430.21442726X-RAY DIFFRACTION100
2.2091-2.37970.25121450.20772757X-RAY DIFFRACTION100
2.3797-2.61920.25571450.20512740X-RAY DIFFRACTION100
2.6192-2.99820.22141450.19792753X-RAY DIFFRACTION99
2.9982-3.77730.25781440.18322736X-RAY DIFFRACTION99
3.7773-65.58360.19681470.17032792X-RAY DIFFRACTION99

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