+Open data
-Basic information
Entry | Database: PDB / ID: 7a04 | ||||||
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Title | Structure of human CKa1 in complex with compound b | ||||||
Components | Choline kinase alpha | ||||||
Keywords | TRANSFERASE / Choline kinase / drugs / cancer / anti proliferative effect / half molecules | ||||||
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 / protein homodimerization activity / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Serran-Aguilera, L. / Mariotto, E. / Rubbini, G. / Castro Navas, F.C. / Marco, C. / Carrasco-Jimenez, M.P. / Ballarotto, M. / Macchiarulo, A. / Hurtado-Guerrero, R. / Viola, G. / Lopez-Cara, L.C. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2020 Title: Synthesis, biological evaluation, in silico modeling and crystallization of novel small monocationic molecules with potent antiproliferative activity by dual mechanism. Authors: Serran-Aguilera, L. / Mariotto, E. / Rubbini, G. / Castro Navas, F.F. / Marco, C. / Carrasco-Jimenez, M.P. / Ballarotto, M. / Macchiarulo, A. / Hurtado-Guerrero, R. / Viola, G. / Lopez-Cara, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a04.cif.gz | 165.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a04.ent.gz | 126.8 KB | Display | PDB format |
PDBx/mmJSON format | 7a04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/7a04 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/7a04 | HTTPS FTP |
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-Related structure data
Related structure data | 7a06C 3g15S S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 81 - 455 / Label seq-ID: 7 - 381
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-Components
#1: Protein | Mass: 44954.457 Da / Num. of mol.: 2 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 | ChemComp-EDO / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG3350, potassium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. obs: 48047 / % possible obs: 99.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.15→2.27 Å / Rmerge(I) obs: 0.715 / Num. unique obs: 6883 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3G15 Resolution: 2.15→19.98 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.639 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.184 / 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: 36.779 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→19.98 Å
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Refine LS restraints |
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