[English] 日本語
![](img/lk-miru.gif)
- PDB-7nb2: Crystal structure of human choline alpha in complex with an inhibitor -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7nb2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human choline alpha in complex with an inhibitor | ||||||
![]() | Choline kinase alpha | ||||||
![]() | TRANSFERASE / PHOSPHATIDYLCHOLINE / INHIBITOR COMPLEX | ||||||
Function / homology | ![]() ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity ...ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / lipid droplet disassembly / phosphatidylcholine biosynthetic process / cholinesterase activity / lipid transport / Synthesis of PC / cellular response to glucose starvation / lipid droplet / lipid metabolic process / protein tyrosine kinase activity / protein homodimerization activity / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Casale, E. / Fasolini, M. | ||||||
![]() | ![]() Title: Identification of unprecedented ATP-competitive choline kinase inhibitors. Authors: Quartieri, F. / Nesi, M. / Avanzi, N.R. / Borghi, D. / Casale, E. / Corti, E. / Cucchi, U. / Donati, D. / Fasolini, M. / Felder, E.R. / Galvani, A. / Giorgini, M.L. / Lomolino, A. / ...Authors: Quartieri, F. / Nesi, M. / Avanzi, N.R. / Borghi, D. / Casale, E. / Corti, E. / Cucchi, U. / Donati, D. / Fasolini, M. / Felder, E.R. / Galvani, A. / Giorgini, M.L. / Lomolino, A. / Menichincheri, M. / Orrenius, C. / Perrera, C. / Re Depaolini, S. / Riccardi-Sirtori, F. / Salsi, E. / Isacchi, A. / Gnocchi, P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 165.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7nb1C ![]() 7nb3C ![]() 2ckqS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 45011.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: GLY 74 EXPRESSION TAG / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P35790, choline kinase, ethanolamine kinase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.5 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 18-20% Peg-mme 5000, 0.1 M Magnesium Formate, 0.1 M HEPES pH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→55.59 Å / Num. obs: 35130 / % possible obs: 99.7 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.689 / Num. unique obs: 3644 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2CKQ Resolution: 2.4→51.196 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.179 / SU B: 9.759 / SU ML: 0.218 / Average fsc free: 0.8712 / Average fsc work: 0.8921 / Cross valid method: NONE / ESU R: 0.38 / ESU R Free: 0.254 Details: Hydrogens have been used if present in the input file
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.682 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→51.196 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|