+
Open data
-
Basic information
Entry | Database: PDB / ID: 5tf9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of WNK1 in complex with Mn2+AMPPNP and WNK476 | ||||||
![]() | Serine/threonine-protein kinase WNK1 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Serine-threonine-protein kinase / ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() 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 / 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 / cellular hyperosmotic response / 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xie, X. / Gunawan, J. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 126.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 95.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3fpq S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31893.912 Da / Num. of mol.: 2 / Fragment: UNP residues 206-483 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9H4A3, ![]() |
---|
-Non-polymers , 5 types, 97 molecules ![](data/chem/img/7AV.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ANP.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.95 % |
---|---|
Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES, pH 7.5, 200 mM calcium acetate, 22% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 30, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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 |
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3FPQ ![]() 3fpq Resolution: 2.5→40.027 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.08
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.98 Å2 / Biso mean: 46.0336 Å2 / Biso min: 22.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→40.027 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %
|