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- PDB-5tf9: Crystal structure of WNK1 in complex with Mn2+AMPPNP and WNK476 -

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Basic information

Entry
Database: PDB / ID: 5tf9
TitleCrystal structure of WNK1 in complex with Mn2+AMPPNP and WNK476
ComponentsSerine/threonine-protein kinase WNK1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Serine-threonine-protein kinase / inhibitor / ternary / complex / allosteric / 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 / negative regulation of sodium ion transport / regulation of mRNA export from nucleus ...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 / negative regulation of sodium ion transport / 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 ion homeostasis / cellular hyperosmotic response / cellular response to chemokine / negative regulation of leukocyte cell-cell adhesion / regulation of monoatomic cation transmembrane transport / cell volume homeostasis / negative regulation of protein localization to plasma membrane / negative regulation of GTPase activity / intracellular non-membrane-bounded organelle / protein kinase activator activity / sodium ion transmembrane transport / neuron development / phosphatase binding / monoatomic ion transport / regulation of sodium ion transport / negative regulation of protein ubiquitination / molecular condensate scaffold activity / negative regulation of autophagy / peptidyl-threonine phosphorylation / Stimuli-sensing channels / mitotic spindle / positive regulation of canonical Wnt signaling pathway / positive regulation of angiogenesis / heart development / T cell receptor signaling pathway / peptidyl-serine phosphorylation / 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 / 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-7AV / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Serine/threonine-protein kinase WNK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXie, X. / Gunawan, J.
CitationJournal: ACS Chem. Biol. / Year: 2016
Title: Discovery and Characterization of Allosteric WNK Kinase Inhibitors.
Authors: Yamada, K. / Zhang, J.H. / Xie, X. / Reinhardt, J. / Xie, A.Q. / LaSala, D. / Kohls, D. / Yowe, D. / Burdick, D. / Yoshisue, H. / Wakai, H. / Schmidt, I. / Gunawan, J. / Yasoshima, K. / Yue, ...Authors: Yamada, K. / Zhang, J.H. / Xie, X. / Reinhardt, J. / Xie, A.Q. / LaSala, D. / Kohls, D. / Yowe, D. / Burdick, D. / Yoshisue, H. / Wakai, H. / Schmidt, I. / Gunawan, J. / Yasoshima, K. / Yue, Q.K. / Kato, M. / Mogi, M. / Idamakanti, N. / Kreder, N. / Drueckes, P. / Pandey, P. / Kawanami, T. / Huang, W. / Yagi, Y.I. / Deng, Z. / Park, H.M.
History
DepositionSep 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,9029
Polymers63,7882
Non-polymers2,1147
Water1,62190
1
A: Serine/threonine-protein kinase WNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9715
Polymers31,8941
Non-polymers1,0774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-14 kcal/mol
Surface area15080 Å2
MethodPISA
2
B: Serine/threonine-protein kinase WNK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9314
Polymers31,8941
Non-polymers1,0373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-7 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.065, 104.482, 69.604
Angle α, β, γ (deg.)90.000, 116.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Serine/threonine-protein kinase WNK1 / Erythrocyte 65 kDa protein / p65 / Kinase deficient protein / Protein kinase lysine-deficient 1 / ...Erythrocyte 65 kDa protein / p65 / Kinase deficient protein / Protein kinase lysine-deficient 1 / Protein kinase with no lysine 1 / hWNK1


Mass: 31893.912 Da / Num. of mol.: 2 / Fragment: UNP residues 206-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WNK1, HSN2, KDP, KIAA0344, PRKWNK1 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q9H4A3, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 97 molecules

#2: Chemical ChemComp-7AV / {2-[(4-chlorophenyl)methoxy]phenyl}{5-[2-(methylamino)-1,3-thiazol-4-yl]-2,3-dihydro-1H-indol-1-yl}methanone


Mass: 475.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H22ClN3O2S
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 200 mM calcium acetate, 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 18658 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 43.83 Å2 / Rmerge(I) obs: 0.086 / Χ2: 1.175 / Net I/av σ(I): 14.844 / Net I/σ(I): 12.2 / Num. measured all: 68621
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.5-2.543.50.4681100
2.54-2.593.60.43199.9
2.59-2.643.60.371100
2.64-2.693.60.331100
2.69-2.753.70.311100
2.75-2.823.70.2531100
2.82-2.893.70.2341100
2.89-2.963.70.2011100
2.96-3.053.70.183199.9
3.05-3.153.70.161100
3.15-3.263.70.1341100
3.26-3.393.70.1121100
3.39-3.553.70.0911100
3.55-3.733.70.081199.9
3.73-3.973.70.074199.9
3.97-4.273.70.068199.9
4.27-4.73.70.064199.9
4.7-5.383.80.061100
5.38-6.783.80.058199.9
6.78-503.60.041199.8

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FPQ

3fpq
PDB Unreleased entry


Resolution: 2.5→40.027 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.08
RfactorNum. reflection% reflection
Rfree0.2658 872 4.73 %
Rwork0.1949 --
obs0.198 18442 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.98 Å2 / Biso mean: 46.0336 Å2 / Biso min: 22.51 Å2
Refinement stepCycle: final / Resolution: 2.5→40.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4238 0 131 90 4459
Biso mean--50.8 41.65 -
Num. residues----528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084457
X-RAY DIFFRACTIONf_angle_d1.0146011
X-RAY DIFFRACTIONf_chiral_restr0.065656
X-RAY DIFFRACTIONf_plane_restr0.004743
X-RAY DIFFRACTIONf_dihedral_angle_d27.3691677
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.65660.33061690.257329063075
2.6566-2.86170.33591450.235129043049
2.8617-3.14960.33691390.230829423081
3.1496-3.60510.26631720.20328813053
3.6051-4.5410.24111410.16929373078
4.541-40.03230.20351060.17530003106

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