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Yorodumi- PDB-1ld7: Co-crystal structure of Human Farnesyltransferase with farnesyldi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ld7 | |||||||||
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Title | Co-crystal structure of Human Farnesyltransferase with farnesyldiphosphate and inhibitor compound 66 | |||||||||
Components | (protein farnesyltransferase ...) x 2 | |||||||||
Keywords | TRANSFERASE / alpha-alpha barrel / inhibitor / ftase / pftase / fpp / caax / ras | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Taylor, J.S. / Terry, K.L. / Beese, L.S. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ld7.cif.gz | 176.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ld7.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ld7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ld7_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1ld7_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1ld7_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 1ld7_validation.cif.gz | 49.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/1ld7 ftp://data.pdbj.org/pub/pdb/validation_reports/ld/1ld7 | HTTPS FTP |
-Related structure data
Related structure data | 1ld8C 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 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.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) 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.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) 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 , 4 types, 523 molecules
#4: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-FPP / |
#6: Chemical | ChemComp-U66 / ( |
#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: 3.17 Å3/Da / Density % sol: 61.26 % | ||||||||||||||||||||||||
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 21, 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: 2→36.74 Å / Num. all: 76934 / Num. obs: 76934 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.138 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.13 Å / % possible all: 79.7 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 75509 / % possible obs: 94.7 % / Num. measured all: 211060 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 60 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JCQ Resolution: 2→36.74 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2465250.94 / 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: 57.8187 Å2 / ksol: 0.400636 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→36.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor obs: 0.194 / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.194 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.38 / Rfactor Rwork: 0.362 / Rfactor obs: 0.362 |