+Open data
-Basic information
Entry | Database: PDB / ID: 3n45 | ||||||
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Title | Human FPPS complex with FBS_04 and zoledronic acid/MG2+ | ||||||
Components | FARNESYL PYROPHOSPHATE SYNTHASE | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / BISPHOSPHONATE / FRAGMENT-BASED SCREENING / TRANSFERASE / ISOPRENE BIOSYNTHESIS / CHOLESTEROL BIOSYNTHESIS / TRANSFERASE-TRANSFERASE INHIBIATOR 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.88 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 | 3n45.cif.gz | 89.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n45.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 3n45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n45_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3n45_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3n45_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 3n45_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/3n45 ftp://data.pdbj.org/pub/pdb/validation_reports/n4/3n45 | HTTPS FTP |
-Related structure data
Related structure data | 3n1vC 3n1wC 3n3lC 3n46C 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, 163 molecules
#2: Chemical | ChemComp-3N3 / ( | ||||
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#3: Chemical | ChemComp-ZOL / | ||||
#4: Chemical | #5: Chemical | #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: 2.59 Å3/Da / Density % sol: 52.57 % |
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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, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 96 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97933 Å |
Detector | Type: MARCCD165 / Detector: CCD / Date: Apr 15, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→50 Å / Num. all: 34881 / Num. obs: 34881 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Biso Wilson estimate: 50.295 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.62 |
Reflection shell | Resolution: 1.88→1.96 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 7.2 / Num. measured obs: 57339 / Num. unique all: 4032 / Num. unique obs: 4032 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.88→40.03 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.84 / FOM work R set: 0.841 / Data cutoff high absF: 2052337 / 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: 50.126 Å2 / ksol: 0.375 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.98 Å2 / Biso mean: 51.067 Å2 / Biso min: 34.17 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.88→40.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→2 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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