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Open data
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Basic information
Entry | Database: PDB / ID: 8wd0 | ||||||
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Title | Crystal structure of T2R-TTL-Erianin complex | ||||||
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![]() | CELL CYCLE / Microtubule | ||||||
Function / homology | ![]() microtubule depolymerization / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / mitotic cell cycle / growth cone ...microtubule depolymerization / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / mitotic cell cycle / growth cone / microtubule / neuron projection / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The cytotoxic natural compound erianin binds to colchicine site of beta-tubulin and overcomes taxane resistance Authors: Yan, W. / Zhou, Y. / Yuan, X. / Bai, P. / Tang, M. / Chen, L. / Wei, H. / Yang, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 452.6 KB | Display | ![]() |
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PDB format | ![]() | 357.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 957.1 KB | Display | ![]() |
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Full document | ![]() | 1002.6 KB | Display | |
Data in XML | ![]() | 80.2 KB | Display | |
Data in CIF | ![]() | 105.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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Components
-Protein , 4 types, 6 molecules ACBDEF
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | | Mass: 22125.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | | Mass: 43825.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 9 types, 82 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | #8: Chemical | ChemComp-GOL / | #9: Chemical | ChemComp-MES / | #10: Chemical | Mass: 318.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22O5 / Feature type: SUBJECT OF INVESTIGATION #11: Chemical | ChemComp-GDP / | #12: Chemical | ChemComp-ACP / | #13: 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: 3.02 Å3/Da / Density % sol: 59.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 6% poly(ethylene glycol) 4000, 8% glycerol, 0.1 M MES (pH 6.7), 30 mM CaCl2 and 30 mM MgCl2. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→38.26 Å / Num. obs: 91318 / % possible obs: 99 % / Redundancy: 13.1 % / Biso Wilson estimate: 61.85 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.6→2.67 Å / Num. unique obs: 1085 / CC1/2: 0.999 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 68.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→38.26 Å
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Refine LS restraints |
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LS refinement shell |
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