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- PDB-1d8d: CO-CRYSTAL STRUCTURE OF RAT PROTEIN FARNESYLTRANSFERASE COMPLEXED... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d8d | ||||||
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Title | CO-CRYSTAL STRUCTURE OF RAT PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH A K-RAS4B PEPTIDE SUBSTRATE AND FPP ANALOG AT 2.0A RESOLUTION | ||||||
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Function / homology | ![]() Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Long, S.B. / Casey, P.J. / Beese, L.S. | ||||||
![]() | ![]() Title: The basis for K-Ras4B binding specificity to protein farnesyltransferase revealed by 2 A resolution ternary complex structures. Authors: Long, S.B. / Casey, P.J. / Beese, L.S. #1: ![]() Title: Crystal Structure of Protein Farnesyltransferase at 2.25A Resolution Authors: Park, H.-W. / Boduluri, S.R. / Moomaw, J.F. / Casey, P.J. / Beese, L.S. #2: ![]() Title: Co-crystal Structure of Mammalian Protein Farnesyltransferase with a Farnesyl Diphosphate Substrate Authors: Long, S.B. / Casey, P.J. / Beese, L.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.1 KB | Display | ![]() |
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PDB format | ![]() | 134.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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
-Farnesyltransferase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 44098.145 Da / Num. of mol.: 1 / Fragment: alpha subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 48722.281 Da / Num. of mol.: 1 / Fragment: beta subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules P
#3: Protein/peptide | Mass: 1298.723 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This synthetic peptide is derived from human K-Ras4B, residues 178-188. References: UniProt: P01116 |
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-Non-polymers , 4 types, 453 molecules ![](data/chem/img/ZN.gif)
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#4: Chemical | ChemComp-ZN / | ||||
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#5: Chemical | ChemComp-ACT / ![]() #6: Chemical | ChemComp-FII / [( | #7: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.35 % | ||||||||||||||||||||
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Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: Peg 8000, ammonium acetate, DTT, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 96 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 23, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→35 Å / Num. all: 77998 / Num. obs: 76088 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2→2.02 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.197 / Num. unique all: 2154 / % possible all: 83.9 |
Reflection | *PLUS Num. measured all: 320401 |
Reflection shell | *PLUS % possible obs: 83.9 % |
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Processing
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Refinement | Resolution: 2→35 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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