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- PDB-5ksx: Crystal structure of human FPPS in complex with an allosteric inh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ksx | ||||||
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Title | Crystal structure of human FPPS in complex with an allosteric inhibitor AM-02-072 | ||||||
![]() | Farnesyl pyrophosphate synthase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Park, J. / Matralis, A. / Tsantrizos, Y.S. / Berghuis, A.M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.9 KB | Display | ![]() |
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PDB format | ![]() | 122.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 947.6 KB | Display | ![]() |
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Full document | ![]() | 953.9 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5juzC ![]() 5jv0C ![]() 5jv1C ![]() 5jv2C ![]() 4xqrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase | ||
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#2: Chemical | ChemComp-PO4 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.75 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 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: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→55.24 Å / Num. obs: 14007 / % possible obs: 99.8 % / Redundancy: 12.5 % / Biso Wilson estimate: 41.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 2.65→2.72 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.037 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.748 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XQR Resolution: 2.65→55.24 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.925 / SU B: 25.637 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.555 / ESU R Free: 0.303 / 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: 62.585 Å2
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Refinement step | Cycle: 1 / Resolution: 2.65→55.24 Å
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Refine LS restraints |
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