+Open data
-Basic information
Entry | Database: PDB / ID: 5w6o | ||||||
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Title | Choline Kinase Alpha in Complex with TCD-717 | ||||||
Components | Choline kinase alpha | ||||||
Keywords | TRANSFERASE/INHIBITOR / enzyme / inhibitor / drug / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å | ||||||
Authors | Kall, S.K. / Lavie, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2018 Title: Identification of a Unique Inhibitor-Binding Site on Choline Kinase alpha. Authors: Kall, S.L. / Delikatny, E.J. / Lavie, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w6o.cif.gz | 163.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w6o.ent.gz | 134.2 KB | Display | PDB format |
PDBx/mmJSON format | 5w6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/5w6o ftp://data.pdbj.org/pub/pdb/validation_reports/w6/5w6o | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 44463.902 Da / Num. of mol.: 2 / Fragment: UNP residues 80-457 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHKA, CHK, CKI / Production host: Escherichia coli (E. coli) References: UniProt: P35790, choline kinase, ethanolamine kinase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5 18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→30 Å / Num. obs: 38250 / % possible obs: 98.6 % / Redundancy: 4.88 % / Net I/σ(I): 13.35 |
-Processing
Software |
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Refinement | Resolution: 2.35→89.54 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.916 / SU B: 13.012 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 0.37 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 53.832 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→89.54 Å
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Refine LS restraints |
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