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Yorodumi- PDB-2h6h: Y365F Protein Farnesyltransferase Mutant Complexed with a Farnesy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h6h | |||||||||
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Title | Y365F Protein Farnesyltransferase Mutant Complexed with a Farnesylated DDPTASACVLS Peptide Product at 1.8A | |||||||||
Components |
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Keywords | TRANSFERASE / FTase / farnesyltransferase / farnesyl transferase / prenyltransferase / CaaX / Ras / lipid modification / prenylation / substrate selectivity | |||||||||
Function / homology | Function and homology information positive regulation of deacetylase activity / skeletal muscle acetylcholine-gated channel clustering / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / protein farnesylation / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity ...positive regulation of deacetylase activity / skeletal muscle acetylcholine-gated channel clustering / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein geranylgeranyltransferase type I / protein farnesylation / 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 / microtubule associated complex / Apoptotic cleavage of cellular proteins / positive regulation of Rac protein signal transduction / alpha-tubulin binding / transforming growth factor beta receptor signaling pathway / lipid metabolic process / receptor tyrosine kinase binding / RAS processing / Inactivation, recovery and regulation of the phototransduction cascade / microtubule binding / Potential therapeutics for SARS / molecular adaptor activity / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Terry, K.L. / Beese, L.S. | |||||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Conversion of protein farnesyltransferase to a geranylgeranyltransferase. Authors: Terry, K.L. / Casey, P.J. / 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 | 2h6h.cif.gz | 182.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h6h.ent.gz | 137.9 KB | Display | PDB format |
PDBx/mmJSON format | 2h6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/2h6h ftp://data.pdbj.org/pub/pdb/validation_reports/h6/2h6h | HTTPS FTP |
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-Related structure data
Related structure data | 2h6fC 2h6gC 2h6iC 1jcqS 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: 44864.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Human FTase alpha subunit / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 References: UniProt: P49354, protein farnesyltransferase, protein geranylgeranyltransferase type I |
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#2: Protein | Mass: 48806.406 Da / Num. of mol.: 1 / Mutation: Y365F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Human FTase beta subunit / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P49356, protein farnesyltransferase |
-Protein/peptide / Sugars , 2 types, 2 molecules P
#3: Protein/peptide | Mass: 1078.152 Da / Num. of mol.: 1 Fragment: residues 173-180 of Rap2a, residues187-189 of H-Ras Mutation: C176T, C177A / Source method: obtained synthetically / Details: Chemically synthesized |
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#4: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose / |
-Non-polymers , 4 types, 711 molecules
#5: Chemical | ChemComp-ACY / |
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#6: Chemical | ChemComp-ZN / |
#7: Chemical | ChemComp-FAR / |
#8: 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: 3.35 Å3/Da / Density % sol: 63.26 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 14% PEG 8000, 200 mM ammonium acetate pH 5.2, 20 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.067401 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2005 / Details: platinum-coated 1:1 focusing toroidal mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.067401 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 109035 / Num. obs: 109005 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Biso Wilson estimate: 17.7 Å2 / Rsym value: 0.089 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 6.5 / Num. unique all: 10850 / Rsym value: 0.516 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JCQ Resolution: 1.8→49.59 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 20.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→49.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.007
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