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Yorodumi- PDB-1sa5: Rat protein farnesyltransferase complexed with FPP and BMS-214662 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sa5 | ||||||
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Title | Rat protein farnesyltransferase complexed with FPP and BMS-214662 | ||||||
Components |
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Keywords | TRANSFERASE / FTASE / FARNESYLTRANSFERASE / FARNESYL TRANSFERASE / CAAX / RAS / CANCER / TUMOR REGRESSION / BMS-214662 / FTI / CLINICAL CANDIDATE / INHIBITOR / PROTEIN PRENYLATION / LIPID MODIFICATION | ||||||
Function / homology | Function and homology information Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / acetylcholine receptor regulator activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / protein geranylgeranyltransferase type I / regulation of fibroblast proliferation ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / acetylcholine receptor regulator 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 / farnesyltranstransferase activity / negative regulation of nitric-oxide synthase biosynthetic process / microtubule associated complex / positive regulation of nitric-oxide synthase biosynthetic process / alpha-tubulin binding / response to inorganic substance / positive regulation of cell cycle / response to cytokine / wound healing / lipid metabolic process / response to organic cyclic compound / receptor tyrosine kinase binding / 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: 2.6 Å | ||||||
Authors | Reid, T.S. / Beese, L.S. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Crystal Structures of the Anticancer Clinical Candidates R115777 (Tipifarnib) and BMS-214662 Complexed with Protein Farnesyltransferase Suggest a Mechanism of FTI Selectivity. Authors: Reid, T.S. / 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 | 1sa5.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sa5.ent.gz | 130.3 KB | Display | PDB format |
PDBx/mmJSON format | 1sa5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/1sa5 ftp://data.pdbj.org/pub/pdb/validation_reports/sa/1sa5 | HTTPS FTP |
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-Related structure data
Related structure data | 1sa4C 1d8dS S: Starting model for refinement 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 , 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 , 5 types, 284 molecules
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-FPP / |
#5: Chemical | ChemComp-BMV / |
#6: Chemical | ChemComp-ACY / |
#7: 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: 3.12 Å3/Da / Density % sol: 60.54 % |
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Crystal grow | Temperature: 290 K / pH: 5.7 Details: 14% PEG 8000, 400 mM ammonium acetate pH 5.7, 20 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 5.70 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2003 / Details: PT-COATED TOROIDAL SI MIRROR |
Radiation | Monochromator: SI CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 35102 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.8 Å2 / Rsym value: 0.11 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.313 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1D8D Resolution: 2.6→49.21 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4021778.96 / 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: 36.2309 Å2 / ksol: 0.393751 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→49.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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