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Yorodumi- PDB-8bi5: Crystal structure of human Choline Kinase A in complex with UNC0737 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bi5 | ||||||
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Title | Crystal structure of human Choline Kinase A in complex with UNC0737 | ||||||
Components | Choline kinase alpha | ||||||
Keywords | STRUCTURAL GENOMICS / Inhibitor / Structural Genomics Consortium / SGC | ||||||
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: 2.5 Å | ||||||
Authors | Diaz-Saez, L. / Ward, J. / Kennedy, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Huber, K. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: To Be Published Title: Crystal structure of human Choline Kinase A in complex with UNC0737 Authors: Diaz-Saez, L. / Kennedy, E. / von Delf, F. / Knapp, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Huber, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bi5.cif.gz | 175.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bi5.ent.gz | 136.4 KB | Display | PDB format |
PDBx/mmJSON format | 8bi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/8bi5 ftp://data.pdbj.org/pub/pdb/validation_reports/bi/8bi5 | HTTPS FTP |
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-Related structure data
Related structure data | 5eqpS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 52310.871 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 |
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-Non-polymers , 6 types, 356 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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-Details
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: 3.49 Å3/Da / Density % sol: 64.73 % |
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Crystal grow | Temperature: 294 K / Method: evaporation / pH: 6.5 Details: 30% PEG smear low molecular weight, 0.1 M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.25 Å / Num. obs: 51852 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.018 / Rrim(I) all: 0.066 / Χ2: 1.02 / Net I/σ(I): 26.9 / Num. measured all: 670428 |
Reflection shell | Resolution: 2.5→2.58 Å / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.37 / Num. measured all: 57329 / Num. unique obs: 4432 / CC1/2: 0.974 / Rpim(I) all: 0.107 / Rrim(I) all: 0.385 / Χ2: 1.03 / Net I/σ(I) obs: 7.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EQP Resolution: 2.5→46.53 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.805 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.197 / 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: 53.221 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→46.53 Å
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