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- PDB-1ld8: Co-crystal structure of Human Farnesyltransferase with farnesyldi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ld8 | |||||||||
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Title | Co-crystal structure of Human Farnesyltransferase with farnesyldiphosphate and inhibitor compound 49 | |||||||||
![]() | (protein farnesyltransferase ...) x 2 | |||||||||
![]() | TRANSFERASE / alpha-alpha barrel / inhibitor / ftase / pftase / fpp / caax / ras | |||||||||
Function / homology | ![]() positive regulation of deacetylase activity / skeletal muscle acetylcholine-gated channel clustering / 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 ...positive regulation of deacetylase activity / skeletal muscle acetylcholine-gated channel clustering / 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 / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Taylor, J.S. / Terry, K.L. / Beese, L.S. | |||||||||
![]() | ![]() Title: 3-Aminopyrrolidinone farnesyltransferase inhibitors: design of macrocyclic compounds with improved pharmacokinetics and excellent cell potency. Authors: Bell, I.M. / Gallicchio, S.N. / Abrams, M. / Beese, L.S. / Beshore, D.C. / Bhimnathwala, H. / Bogusky, M.J. / Buser, C.A. / Culberson, J.C. / Davide, J. / Ellis-Hutchings, M. / Fernandes, C. ...Authors: Bell, I.M. / Gallicchio, S.N. / Abrams, M. / Beese, L.S. / Beshore, D.C. / Bhimnathwala, H. / Bogusky, M.J. / Buser, C.A. / Culberson, J.C. / Davide, J. / Ellis-Hutchings, M. / Fernandes, C. / Gibbs, J.B. / Graham, S.L. / Hamilton, K.A. / Hartman, G.D. / Heimbrook, D.C. / Homnick, C.F. / Huber, H.E. / Huff, J.R. / Kassahun, K. / Koblan, K.S. / Kohl, N.E. / Lobell, R.B. / Lynch Jr., J.J. / Robinson, R. / Rodrigues, A.D. / Taylor, J.S. / Walsh, E.S. / Williams, T.M. / Zartman, C.B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.7 KB | Display | ![]() |
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PDB format | ![]() | 137.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 35.8 KB | Display | |
Data in CIF | ![]() | 53.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ld7C ![]() 1jcqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein farnesyltransferase ... , 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.) ![]() ![]() ![]() References: UniProt: P49354, Transferases; Transferring alkyl or aryl groups, other than methyl groups |
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#2: Protein | Mass: 48822.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P49356, Transferases; Transferring alkyl or aryl groups, other than methyl groups |
-Sugars , 1 types, 1 molecules
#3: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose |
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-Non-polymers , 5 types, 696 molecules ![](data/chem/img/ACY.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FPP.gif)
![](data/chem/img/U49.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FPP.gif)
![](data/chem/img/U49.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-ZN / | #6: Chemical | ChemComp-FPP / | #7: Chemical | ChemComp-U49 / ( | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.95 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG8K, NH4OAc, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / PH range low: 5.5 / PH range high: 5.3 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 29, 2000 / Details: mirrors |
Radiation | Monochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→31.02 Å / Num. all: 88092 / Num. obs: 88092 / % possible obs: 81.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.5 Å2 |
Reflection shell | Resolution: 1.8→1.91 Å / % possible all: 26.6 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 87139 / % possible obs: 80.5 % / Num. measured all: 242857 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 16 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JCQ Resolution: 1.8→30.85 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2579340.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.8462 Å2 / ksol: 0.403211 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→30.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 50 Å / Rfactor obs: 0.184 / Rfactor Rfree: 0.202 / Rfactor Rwork: 0.184 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.454 / Rfactor Rwork: 0.453 / Rfactor obs: 0.453 |