+Open data
-Basic information
Entry | Database: PDB / ID: 3ksl | ||||||
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Title | Structure of FPT bound to DATFP-DH-GPP | ||||||
Components |
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Keywords | TRANSFERASE / PRENYLTRANSFERASE / Metal-binding / Phosphoprotein / Zinc | ||||||
Function / homology | Function and homology information skeletal muscle acetylcholine-gated channel clustering / Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / positive regulation of tubulin deacetylation ...skeletal muscle acetylcholine-gated channel clustering / Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / regulation of fibroblast proliferation / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / negative regulation of nitric-oxide synthase biosynthetic process / farnesyltranstransferase activity / 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 / : / positive regulation of cell cycle / response to cytokine / wound healing / response to organic cyclic compound / lipid metabolic process / 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 / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.05 Å | ||||||
Authors | Hovlid, M.L. / Edelstein, R.L. / Henry, O. / Ochocki, J. / DeGraw, A. / Lenevich, S. / Talbot, T. / Young, V. / Hruza, A.W. / Lopez-Gallego, F. ...Hovlid, M.L. / Edelstein, R.L. / Henry, O. / Ochocki, J. / DeGraw, A. / Lenevich, S. / Talbot, T. / Young, V. / Hruza, A.W. / Lopez-Gallego, F. / Labello, N.P. / Strickland, C.L. / Schmidt-Dannert, C. / Distefano, M.D. | ||||||
Citation | Journal: Chem.Biol.Drug Des. / Year: 2010 Title: Synthesis, properties, and applications of diazotrifluropropanoyl-containing photoactive analogs of farnesyl diphosphate containing modified linkages for enhanced stability. Authors: Hovlid, M.L. / Edelstein, R.L. / Henry, O. / Ochocki, J. / DeGraw, A. / Lenevich, S. / Talbot, T. / Young, V.G. / Hruza, A.W. / Lopez-Gallego, F. / Labello, N.P. / Strickland, C.L. / Schmidt- ...Authors: Hovlid, M.L. / Edelstein, R.L. / Henry, O. / Ochocki, J. / DeGraw, A. / Lenevich, S. / Talbot, T. / Young, V.G. / Hruza, A.W. / Lopez-Gallego, F. / Labello, N.P. / Strickland, C.L. / Schmidt-Dannert, C. / Distefano, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ksl.cif.gz | 170.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ksl.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ksl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ksl_validation.pdf.gz | 997.4 KB | Display | wwPDB validaton report |
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Full document | 3ksl_full_validation.pdf.gz | 1002.6 KB | Display | |
Data in XML | 3ksl_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 3ksl_validation.cif.gz | 45.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/3ksl ftp://data.pdbj.org/pub/pdb/validation_reports/ks/3ksl | HTTPS FTP |
-Related structure data
Related structure data | 1o1tS S: Starting model for refinement |
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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: 44086.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fnta / Plasmid: PET15B / Production host: Escherichia coli (E. coli) References: UniProt: Q5RKJ4, UniProt: Q04631*PLUS, protein farnesyltransferase |
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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 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: Q02293, protein farnesyltransferase |
-Non-polymers , 4 types, 430 molecules
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-ZN / |
#5: Chemical | ChemComp-SZH / ( |
#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: 3.15 Å3/Da / Density % sol: 61.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: PEG 4000, SODIUM ACETATE, KCL, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 29, 2009 / Details: VARIMAX MULTI-LAYER OPTICS |
Radiation | Monochromator: VARIMAX MULTI-LAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→29.45 Å / Num. all: 72742 / Num. obs: 71190 / % possible obs: 97.9 % / Observed criterion σ(I): 2.5 / Redundancy: 3.8 % / Biso Wilson estimate: 35.33 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1O1T Resolution: 2.05→29.45 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: STANDARD AMINO ACID DICTIONARY. BONDS AND ANGLES FROM ENGH AND HUBER EH99. OTHER VALUES BASED ON PREVIOUS TNT OR TAKEN FROM CCP4.
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Displacement parameters | Biso mean: 36.81 Å2
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Refine analyze | Luzzati coordinate error obs: 0.232 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→29.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.1 Å / Total num. of bins used: 20
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