+Open data
-Basic information
Entry | Database: PDB / ID: 3n46 | ||||||
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Title | Human FPPS complex with NOV_980 and zoledronic acid/MG2+ | ||||||
Components | FARNESYL PYROPHOSPHATE SYNTHASEDimethylallyltranstransferase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / BISPHOSPHONATE / FRAGMENT-BASED SCREENING / TRANSFERASE / ISOPRENE BIOSYNTHESIS / CHOLESTEROL BIOSYNTHESIS / RANSFERASE-TRANSFERASE INHIBITOR complex / 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: 2.35 Å | ||||||
Authors | Rondeau, J.-M. | ||||||
Citation | 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. / Gotte, 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. / Gotte, M. / Bitsch, F. / Hemmig, R. / Henry, C. / Lehmann, S. / Glickman, J.F. / Roddy, T.P. / Stout, S.J. / Green, J.R. #1: Journal: ChemMedChem / Year: 2006 Title: Structural basis for the exceptional in vivo efficacy of bisphosphonate drugs Authors: Rondeau, J.M. / Bitsch, F. / Bourgier, E. / Geiser, M. / Hemmig, R. / Kroemer, M. / Lehmann, S. / Ramage, P. / Rieffel, S. / Strauss, A. / Green, J.R. / Jahnke, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n46.cif.gz | 89.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n46.ent.gz | 66.2 KB | Display | PDB format |
PDBx/mmJSON format | 3n46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/3n46 ftp://data.pdbj.org/pub/pdb/validation_reports/n4/3n46 | HTTPS FTP |
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-Related structure data
Related structure data | 3n1vC 3n1wC 3n3lC 3n45C 3n49C 3n5hC 3n5jC 3n6kC C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules F
#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 (E. coli) / Strain (production host): BL21 TUNER (DE3) References: UniProt: P14324, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase |
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-Non-polymers , 5 types, 144 molecules
#2: Chemical | ChemComp-3N5 / ( | ||||
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#3: Chemical | ChemComp-ZOL / | ||||
#4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: 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: 2.71 Å3/Da / Density % sol: 54.59 % |
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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, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97936 Å |
Detector | Type: MAR CCD 165 / Detector: CCD / Date: Sep 2, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97936 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→100 Å / Num. all: 18838 / Num. obs: 18838 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 51.905 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.99 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 5.7 / Num. measured obs: 9429 / Num. unique all: 1335 / Num. unique obs: 1335 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.35→39.19 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.757 / Data cutoff high absF: 2563747 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.973 Å2 / ksol: 0.361 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.42 Å2 / Biso mean: 59.389 Å2 / Biso min: 25.02 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→39.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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