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Yorodumi- PDB-1nl4: Crystal Structure of Rat Farnesyl Transferase in Complex With A P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nl4 | ||||||
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Title | Crystal Structure of Rat Farnesyl Transferase in Complex With A Potent Biphenyl Inhibitor | ||||||
Components |
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Keywords | TRANSFERASE / Prenyltransferase | ||||||
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 Rac protein signal transduction / 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 / FOURIER SYNTHESIS / Resolution: 2.7 Å | ||||||
Authors | Curtin, M.L. / Florjancic, A.S. / Cohen, J. / Gu, W.-J. / Frost, D.J. / Muchmore, S.W. / Sham, H.L. | ||||||
Citation | Journal: BIOORG.MED.CHEM.LETT. / Year: 2003 Title: Novel and Selective Imidazole-containing Biphenyl Inhibitors of Protein Farnesyltransferase Authors: Curtin, M.L. / Florjancic, A.S. / Cohen, J. / Gu, W.-J. / Frost, D.J. / Muchmore, S.W. / Sham, H.L. | ||||||
History |
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Remark 999 | sequence Author indicates that this represents an inconsequential mutation |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nl4.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nl4.ent.gz | 105.6 KB | Display | PDB format |
PDBx/mmJSON format | 1nl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/1nl4 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/1nl4 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37634.293 Da / Num. of mol.: 1 / Fragment: residue 55-366 / Mutation: I156T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: FNTA / Production host: Escherichia coli (E. coli) References: UniProt: Q04631, Transferases; Transferring alkyl or aryl groups, other than methyl groups |
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#2: Protein | Mass: 44879.297 Da / Num. of mol.: 1 / Fragment: residue 23-423 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: FNTB / Production host: Escherichia coli (E. coli) References: UniProt: Q02293, Transferases; Transferring alkyl or aryl groups, other than methyl groups |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-HFP / |
#5: Chemical | ChemComp-FTL / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: equilibriate equal volumes of 10mg/ml protein stock solution (with 50mM Tris, 1mM DTT, 1mM NaN3, 5 mM ZnCl2-pH 8.2) and well solution containing 100mM KCl, 100mM Sodium Acetate, at pH 4.8, ...Details: equilibriate equal volumes of 10mg/ml protein stock solution (with 50mM Tris, 1mM DTT, 1mM NaN3, 5 mM ZnCl2-pH 8.2) and well solution containing 100mM KCl, 100mM Sodium Acetate, at pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal grow | *PLUS Details: Strickland, C.L., (19999) J. Med. Chem., 42, 2125. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 6, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 26759 / Num. obs: 26759 / % possible obs: 85 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 50 Å / % possible obs: 98 % / Rmerge(I) obs: 0.048 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 5 / σ(I): 3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refinement | *PLUS Highest resolution: 2.8 Å / Rfactor Rfree: 0.321 / Rfactor Rwork: 0.249 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |