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- PDB-7t0d: Cryptococcus neoformans protein farnesyltransferase in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7t0d | ||||||
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Title | Cryptococcus neoformans protein farnesyltransferase in complex with FPP and inhibitor 2k | ||||||
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![]() | Transferase/Inhibitor / Inhibitor / Protein prenylyltransferase / Antifungal / TRANSFERASE / TRANSFERASE-Inhibitor complex | ||||||
Function / homology | ![]() prenylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y. / Shi, Y. / Beese, L.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Guided Discovery of Potent Antifungals that Prevent Ras Signaling by Inhibiting Protein Farnesyltransferase. Authors: Wang, Y. / Xu, F. / Nichols, C.B. / Shi, Y. / Hellinga, H.W. / Alspaugh, J.A. / Distefano, M.D. / 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 | ![]() | 201.6 KB | Display | ![]() |
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PDB format | ![]() | 154.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 39 KB | Display | |
Data in CIF | ![]() | 57.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7t08C ![]() 7t09C ![]() 7t0aC ![]() 7t0bC ![]() 7t0cC ![]() 7t0eC ![]() 8e9eC ![]() 3sfxS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 40913.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_02229 / Production host: ![]() ![]() |
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#2: Protein | Mass: 56806.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_05740 / Production host: ![]() ![]() |
-Non-polymers , 7 types, 617 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/3FX.gif)
![](data/chem/img/XO7.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FPP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/3FX.gif)
![](data/chem/img/XO7.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FPP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | ChemComp-XO7 / ( | #7: Chemical | ChemComp-ZN / | #8: Chemical | ChemComp-FPP / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.34 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 100mM CAPSO pH9.5, 50-75mM Li2SO4, 200mM NaCl, 16%-21% PEG4000. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.906→42.43 Å / Num. obs: 103127 / % possible obs: 99.42 % / Redundancy: 6 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.06259 / Rpim(I) all: 0.02767 / Rrim(I) all: 0.06861 / Net I/σ(I): 15.61 |
Reflection shell | Resolution: 1.906→1.974 Å / Redundancy: 6 % / Rmerge(I) obs: 0.7196 / Mean I/σ(I) obs: 2.59 / Num. unique obs: 9878 / CC1/2: 0.912 / CC star: 0.977 / Rpim(I) all: 0.3161 / Rrim(I) all: 0.7877 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SFX Resolution: 1.906→42.43 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.45 Å2 / Biso mean: 42.6688 Å2 / Biso min: 22.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.906→42.43 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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