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Yorodumi- PDB-3e33: Protein farnesyltransferase complexed with FPP and ethylenediamin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3.0E+33 | ||||||
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Title | Protein farnesyltransferase complexed with FPP and ethylenediamine scaffold inhibitor 7 | ||||||
Components |
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Keywords | TRANSFERASE / FTase / protein farnesyltransferase / farnesyltransferase / malaria / plasmodium / falciparum / antimalarial / inhibitor / ethylenediamine / Prenyltransferase / Metal-binding / Phosphoprotein / Zinc | ||||||
Function / homology | Function and homology information Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / protein geranylgeranyltransferase type I / regulation of fibroblast proliferation / positive regulation of tubulin deacetylation ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / protein geranylgeranyltransferase type I / regulation of fibroblast proliferation / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / farnesyltranstransferase activity / negative regulation of nitric-oxide synthase biosynthetic process / microtubule associated complex / enzyme-linked receptor protein signaling pathway / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of Rac protein signal transduction / alpha-tubulin binding / response to inorganic substance / positive regulation of cell cycle / response to cytokine / wound healing / lipid metabolic process / receptor tyrosine kinase binding / response to organic cyclic compound / positive regulation of fibroblast proliferation / fibroblast proliferation / microtubule binding / cell population proliferation / molecular adaptor activity / negative regulation of cell population proliferation / positive regulation of cell population proliferation / negative regulation of apoptotic process / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hast, M.A. / Beese, L.S. | ||||||
Citation | Journal: Chem.Biol. / Year: 2009 Title: Structural basis for binding and selectivity of antimalarial and anticancer ethylenediamine inhibitors to protein farnesyltransferase. Authors: Hast, M.A. / Fletcher, S. / Cummings, C.G. / Pusateri, E.E. / Blaskovich, M.A. / Rivas, K. / Gelb, M.H. / Van Voorhis, W.C. / Sebti, S.M. / Hamilton, A.D. / Beese, L.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e33.cif.gz | 166.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e33.ent.gz | 129 KB | Display | PDB format |
PDBx/mmJSON format | 3e33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/3e33 ftp://data.pdbj.org/pub/pdb/validation_reports/e3/3e33 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 44098.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fnta / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I |
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#2: Protein | Mass: 48722.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fntb / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q02293, protein farnesyltransferase |
-Non-polymers , 4 types, 233 molecules
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-FPP / |
#5: Chemical | ChemComp-ED7 / |
#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: 3.16 Å3/Da / Density % sol: 61.03 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: ammonium acetate pH 5.7, 12% PEG8000, DTT, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 86658 / Num. obs: 85965 / % possible obs: 99.2 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.9→1.96 Å / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→33.98 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.582 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.397 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→33.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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