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- PDB-7nb1: Crystal structure of human choline alpha in complex with an inhibitor -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nb1 | ||||||
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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 / phosphorylation / 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 167.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 968.5 KB | Display | ![]() |
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Full document | ![]() | 977.1 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 39 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nb2C ![]() 7nb3C ![]() 2ckqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45011.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: GLY 74 IS AN EXPRESSION TAG / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P35790, choline kinase, ethanolamine kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.81 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.4 Å / Num. obs: 40989 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 5891 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2CKQ Resolution: 2.3→44.857 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.184 / SU B: 7.444 / SU ML: 0.174 / Average fsc free: 0.8945 / Average fsc work: 0.9141 / Cross valid method: FREE R-VALUE / ESU R: 0.292 / ESU R Free: 0.229 Details: Hydrogens have been used if present in the input file
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.247 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→44.857 Å
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Refine LS restraints |
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LS refinement shell |
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