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Yorodumi- PDB-6ol2: Crystallography of novel WNK1 and WNK3 inhibitors discovered from... -
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-Basic information
Entry | Database: PDB / ID: 6ol2 | ||||||
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Title | Crystallography of novel WNK1 and WNK3 inhibitors discovered from high-throughput-screening | ||||||
Components | Serine/threonine-protein kinase WNK1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / 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 / monoatomic ion homeostasis ...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 / monoatomic ion homeostasis / regulation of mRNA export from nucleus / positive regulation of potassium ion import across plasma membrane / regulation of sodium ion transmembrane transport / intracellular chloride ion homeostasis / negative regulation of heterotypic cell-cell adhesion / positive regulation of T cell chemotaxis / positive regulation of systemic arterial blood pressure / non-membrane-bounded organelle assembly / potassium ion homeostasis / cellular response to chemokine / potassium channel inhibitor activity / protein serine/threonine kinase inhibitor activity / negative regulation of leukocyte cell-cell adhesion / cellular hyperosmotic response / 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 / negative regulation of autophagy / molecular condensate scaffold activity / modulation of chemical synaptic transmission / mitotic spindle / regulation of blood pressure / positive regulation of angiogenesis / positive regulation of canonical Wnt signaling pathway / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Chlebowicz, J. / Akella, R. / Sekulski, K. / Humphreys, J.M. / Durbacz, M.Z. / He, H. / Rodan, A. / Posner, B. / Goldsmith, E.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystallography of novel WNK1 and WNK3 inhibitors discovered from high throughput screening Authors: Chlebowicz, J. / Akella, R. / Sekulski, K. / Humphreys, J.M. / Durbacz, M.Z. / He, H. / Rodan, A. / Posner, B. / Goldsmith, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ol2.cif.gz | 134.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ol2.ent.gz | 101.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ol2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ol2_validation.pdf.gz | 769.9 KB | Display | wwPDB validaton report |
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Full document | 6ol2_full_validation.pdf.gz | 779.1 KB | Display | |
Data in XML | 6ol2_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 6ol2_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/6ol2 ftp://data.pdbj.org/pub/pdb/validation_reports/ol/6ol2 | HTTPS FTP |
-Related structure data
Related structure data | 5drbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33481.496 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 / Plasmid: pHis / Production host: Escherichia coli (E. coli) References: UniProt: Q9JIH7, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-MU7 / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.75 % / Description: Plates |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG3350, 0.2 M sodium formate |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97905 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2018 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97905 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 18499 / % possible obs: 94.6 % / Redundancy: 3.4 % / Rsym value: 0.08 / Net I/σ(I): 24.1 |
Reflection shell | Highest resolution: 2.1 Å / Redundancy: 2.4 % / Num. unique obs: 600 / Rsym value: 0.541 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5DRB Resolution: 2.1→34.25 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.879 / SU B: 11.202 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.844 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→34.25 Å
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