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Yorodumi- PDB-4l2x: Crystal structure of human FPPS in complex with magnesium, CL0213... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l2x | ||||||
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Title | Crystal structure of human FPPS in complex with magnesium, CL02134, and inorganic pyrophosphate | ||||||
Components | Farnesyl pyrophosphate synthaseDimethylallyltranstransferase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / 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: 2.55 Å | ||||||
Authors | Park, J. / Leung, C.-Y. / Tsantrizos, Y.S. / Berghuis, A.M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Thienopyrimidine Bisphosphonate (ThPBP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Optimization and Characterization of the Mode of Inhibition. Authors: Leung, C.Y. / Park, J. / De Schutter, J.W. / Sebag, M. / 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 | 4l2x.cif.gz | 85.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l2x.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 4l2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/4l2x ftp://data.pdbj.org/pub/pdb/validation_reports/l2/4l2x | HTTPS FTP |
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-Related structure data
Related structure data | 4jvjC 4h5dS 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 | ChemComp-YL2 / ({[ | ||
#3: Chemical | ChemComp-POP / | ||
#4: Chemical | #5: 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: 2.47 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 16% PEG8000, 20% glycerol, 0.16 M magnesium acetate, 0.08 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K |
-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: May 5, 2013 |
Radiation | Monochromator: ACCEL/Bruker DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. all: 14627 / Num. obs: 14376 / % possible obs: 98.3 % / Redundancy: 9.48 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.55→2.62 Å / Redundancy: 9.52 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 6.07 / Num. unique all: 1069 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 4H5D Resolution: 2.55→35.23 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.554 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.56 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 61.961 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→35.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.619 Å / Total num. of bins used: 20
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