+Open data
-Basic information
Entry | Database: PDB / ID: 4cga | ||||||
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Title | Human choline kinase a1 in complex with compound 5 | ||||||
Components | CHOLINE KINASE ALPHA | ||||||
Keywords | TRANSFERASE / CANCER / DRUG TARGET / BISCATIONIC COMPOUNDS | ||||||
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: 1.74 Å | ||||||
Authors | Rubio-Ruiz, B. / Figuerola-Conchas, A. / Ramos-Torrecillas, J. / Capitan-Canadas, F. / Rios-Marco, P. / Carrasco, M.P. / Gallo, M.A. / Espinosa, A. / Marco, C. / Concepcion, C. ...Rubio-Ruiz, B. / Figuerola-Conchas, A. / Ramos-Torrecillas, J. / Capitan-Canadas, F. / Rios-Marco, P. / Carrasco, M.P. / Gallo, M.A. / Espinosa, A. / Marco, C. / Concepcion, C. / Entrena-Guadix, A. / Hurtado-Guerrero, R. / Conejo-Garcia, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Discovery of a New Binding Site on Human Choline Kinase A1: Design, Synthesis, Crystallographic Studies and Biological Evaluation of Asymmetrical Bispyridinium Derivatives Authors: Rubio-Ruiz, B. / Figuerola-Conchas, A. / Ramos-Torrecillas, J. / Capitan-Canadas, F. / Rios-Marco, P. / Carrasco, M.P. / Gallo, M.A. / Espinosa, A. / Marco, C. / Concepcion, C. / Entrena- ...Authors: Rubio-Ruiz, B. / Figuerola-Conchas, A. / Ramos-Torrecillas, J. / Capitan-Canadas, F. / Rios-Marco, P. / Carrasco, M.P. / Gallo, M.A. / Espinosa, A. / Marco, C. / Concepcion, C. / Entrena-Guadix, A. / Hurtado-Guerrero, R. / Conejo-Garcia, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cga.cif.gz | 160.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cga.ent.gz | 126 KB | Display | PDB format |
PDBx/mmJSON format | 4cga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/4cga ftp://data.pdbj.org/pub/pdb/validation_reports/cg/4cga | HTTPS FTP |
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-Related structure data
Related structure data | 4cg8C 4cg9C 3g15S C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 44954.457 Da / Num. of mol.: 1 / Fragment: RESIDUES 75-457 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMALC2X / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR References: UniProt: P35790, choline kinase, ethanolamine kinase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.02 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 73 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.872 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.872 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→20 Å / Num. obs: 44468 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.74→1.83 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.7 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3G15 Resolution: 1.74→220.6 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.145 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
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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: 21.837 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→220.6 Å
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Refine LS restraints |
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