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- PDB-6oag: 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: 6oag | ||||||
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Title | Crystal structure of human FPPS in complex with an allosteric inhibitor YF-02-82 | ||||||
![]() | Farnesyl pyrophosphate synthase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Transferase / 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. / Berghuis, A.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Chirality-Driven Mode of Binding of alpha-Aminophosphonic Acid-Based Allosteric Inhibitors of the Human Farnesyl Pyrophosphate Synthase (hFPPS). Authors: Feng, Y. / Park, J. / Li, S.G. / Boutin, R. / Viereck, P. / Schilling, M.A. / 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 | ![]() | 161.6 KB | Display | ![]() |
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PDB format | ![]() | 126.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1015.4 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n7yC ![]() 6n7zC ![]() 6n82C ![]() 6n83C ![]() 6oahC ![]() 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 on special symmetry positions |
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Components
#1: Protein | Mass: 43144.980 Da / Num. of mol.: 1 / Fragment: 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 | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.45 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.075 M HEPES, 0.6 M potassium phosphate, 0.6 M sodium phosphate, 25% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→76.86 Å / Num. obs: 21951 / % possible obs: 99.6 % / Redundancy: 12.7 % / Biso Wilson estimate: 55.395 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.02 / Rrim(I) all: 0.069 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.631 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1069 / CC1/2: 0.797 / Rpim(I) all: 0.496 / Rrim(I) all: 1.707 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XQR Resolution: 2.3→55.74 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 25.224 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.211 / 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: 80.074 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→55.74 Å
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Refine LS restraints |
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