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Yorodumi- PDB-5juz: Crystal structure of human FPPS in complex with an allosteric inh... -
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-Basic information
Entry | Database: PDB / ID: 5juz | ||||||
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Title | Crystal structure of human FPPS in complex with an allosteric inhibitor CL-06-057 | ||||||
Components | Farnesyl pyrophosphate synthase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding / nucleoplasm / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å | ||||||
Authors | Park, J. / Magder, A. / Leung, C.Y. / Tsantrizos, Y.S. / Berghuis, A.M. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Pharmacophore Mapping of Thienopyrimidine-Based Monophosphonate (ThP-MP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase. Authors: Park, J. / Leung, C.Y. / Matralis, A.N. / Lacbay, C.M. / Tsakos, M. / Fernandez De Troconiz, G. / Berghuis, A.M. / Tsantrizos, Y.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5juz.cif.gz | 154.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5juz.ent.gz | 119.3 KB | Display | PDB format |
PDBx/mmJSON format | 5juz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/5juz ftp://data.pdbj.org/pub/pdb/validation_reports/ju/5juz | HTTPS FTP |
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-Related structure data
Related structure data | 5jv0C 5jv1C 5jv2C 5ksxC 4qxsS 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: 43144.980 Da / Num. of mol.: 1 / Fragment: UNP residues 67-419 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Production host: Escherichia coli (E. coli) References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase | ||||
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#2: Chemical | #3: Chemical | ChemComp-YL4 / [( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.17 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.6 M sodium phosphate, 0.6 M potassium phosphate, 25% glycerol, 0.075 M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→78.42 Å / Num. obs: 19304 / % possible obs: 99.8 % / Redundancy: 9.3 % / Biso Wilson estimate: 46.933 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 2.3 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4QXS Resolution: 2.4→78.42 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 19.608 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.215 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.524 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→78.42 Å
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Refine LS restraints |
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