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Open data
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Basic information
Entry | Database: PDB / ID: 8cld | ||||||||||||
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Title | Ansamitocin P3 bound to tubulin (T2R-TTL) complex | ||||||||||||
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![]() | CELL CYCLE / Drug-tubulin-complex Cell cycle inhibition | ||||||||||||
Function / homology | ![]() positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development ...positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / nervous system development / mitotic cell cycle / growth cone / microtubule / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Wranik, M. / Kepa, M.W. / Bertrand, Q. / Weinert, T. / Steinmetz, M. / Standfuss, J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers. Authors: Wranik, M. / Kepa, M.W. / Beale, E.V. / James, D. / Bertrand, Q. / Weinert, T. / Furrer, A. / Glover, H. / Gashi, D. / Carrillo, M. / Kondo, Y. / Stipp, R.T. / Khusainov, G. / Nass, K. / ...Authors: Wranik, M. / Kepa, M.W. / Beale, E.V. / James, D. / Bertrand, Q. / Weinert, T. / Furrer, A. / Glover, H. / Gashi, D. / Carrillo, M. / Kondo, Y. / Stipp, R.T. / Khusainov, G. / Nass, K. / Ozerov, D. / Cirelli, C. / Johnson, P.J.M. / Dworkowski, F. / Beale, J.H. / Stubbs, S. / Zamofing, T. / Schneider, M. / Krauskopf, K. / Gao, L. / Thorn-Seshold, O. / Bostedt, C. / Bacellar, C. / Steinmetz, M.O. / Milne, C. / Standfuss, 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 | ![]() | 881.1 KB | Display | ![]() |
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PDB format | ![]() | 727.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 44.6 KB | Display | |
Data in CIF | ![]() | 65 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cl5C ![]() 8cl6C ![]() 8cl7C ![]() 8cl8C ![]() 8cl9C ![]() 8clbC ![]() 8clcC ![]() 8cleC ![]() 8clfC ![]() 8clgC ![]() 8clhC C: citing same article ( |
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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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1 |
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Unit cell |
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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: 44378.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 14 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/BKF.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/BKF.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-BKF / ( | #10: Chemical | ChemComp-ACP / | #11: 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: 3.1 Å3/Da / Density % sol: 60.35 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 6.5 Details: 6% PEG4000 (w/v), 30 mM MgCl2, 30 mM CaCl2, 0.1 M MES/Imidazole, 5 mM L-tyrosine |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Feb 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→15.17 Å / Num. obs: 56426 / % possible obs: 100 % / Redundancy: 38.5 % / CC1/2: 0.776 / Net I/σ(I): 3.38 |
Reflection shell | Resolution: 3.1→3.2 Å / Mean I/σ(I) obs: 1.25 / Num. unique obs: 5544 / CC1/2: 0.42 |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: Hydroxyethylcellulose / Description: High-viscosity injection / Injector diameter: 75 µm |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 3.2→15.1 Å
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