+Open data
-Basic information
Entry | Database: PDB / ID: 5dgn | ||||||
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Title | Crystal structure of human FPPS in complex with compound 13 | ||||||
Components | Farnesyl pyrophosphate synthaseDimethylallyltranstransferase | ||||||
Keywords | TRANSFERASE / ISOPRENE BIOSYNTHESIS / CHOLESTEROL BIOSYNTHESIS | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.08 Å | ||||||
Authors | Rondeau, J.M. / Bourgier, E. / Lehmann, S. | ||||||
Citation | Journal: Chemmedchem / Year: 2015 Title: Discovery of Novel Allosteric Non-Bisphosphonate Inhibitors of Farnesyl Pyrophosphate Synthase by Integrated Lead Finding. Authors: Marzinzik, A.L. / Amstutz, R. / Bold, G. / Bourgier, E. / Cotesta, S. / Glickman, J.F. / Gotte, M. / Henry, C. / Lehmann, S. / Hartwieg, J.C. / Ofner, S. / Pelle, X. / Roddy, T.P. / Rondeau, ...Authors: Marzinzik, A.L. / Amstutz, R. / Bold, G. / Bourgier, E. / Cotesta, S. / Glickman, J.F. / Gotte, M. / Henry, C. / Lehmann, S. / Hartwieg, J.C. / Ofner, S. / Pelle, X. / Roddy, T.P. / Rondeau, J.M. / Stauffer, F. / Stout, S.J. / Widmer, A. / Zimmermann, J. / Zoller, T. / Jahnke, W. #1: Journal: Nat. Chem. Biol. / Year: 2010 Title: Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery Authors: Jahnke, W. / Rondeau, J.M. / Cotesta, S. / Marzinzik, A. / Pelle, X. / Geiser, M. / Strauss, A. / Goette, M. / Bitsch, F. / Hemmig, R. / Henry, C. / Lehmann, S. / Glickman, J.F. / Roddy, T.P. ...Authors: Jahnke, W. / Rondeau, J.M. / Cotesta, S. / Marzinzik, A. / Pelle, X. / Geiser, M. / Strauss, A. / Goette, M. / Bitsch, F. / Hemmig, R. / Henry, C. / Lehmann, S. / Glickman, J.F. / Roddy, T.P. / Stout, S.J. / Green, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dgn.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dgn.ent.gz | 123.9 KB | Display | PDB format |
PDBx/mmJSON format | 5dgn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/5dgn ftp://data.pdbj.org/pub/pdb/validation_reports/dg/5dgn | HTTPS FTP |
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-Related 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: 40183.855 Da / Num. of mol.: 1 / Fragment: residues 72-419 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Tuner References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase |
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#2: Chemical | ChemComp-59Y / |
#3: 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: 2.9 Å3/Da / Density % sol: 57.57 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.3 / Details: 1.2M sodium potassium phosphate, 25% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Aug 15, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.08→78 Å / Num. obs: 28256 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Biso Wilson estimate: 32.75 Å2 / Rmerge F obs: 0.09 / Rmerge(I) obs: 0.117 / Rrim(I) all: 0.122 / Net I/σ(I): 14.63 / Num. measured all: 346184 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.08→25.57 Å / Cor.coef. Fo:Fc: 0.9468 / Cor.coef. Fo:Fc free: 0.9235 / SU R Cruickshank DPI: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.168 / SU Rfree Blow DPI: 0.153 / SU Rfree Cruickshank DPI: 0.153
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Displacement parameters | Biso max: 172.13 Å2 / Biso mean: 59.73 Å2 / Biso min: 17.08 Å2
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Refine analyze | Luzzati coordinate error free: 0.329 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.08→25.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.16 Å / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Details: FPPS / Origin x: 10.2137 Å / Origin y: 79.67 Å / Origin z: 27.4951 Å
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Refinement TLS group | Selection: all / Selection details: { F|* } |