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Open data
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Basic information
Entry | Database: PDB / ID: 5bmv | ||||||
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Title | CRYSTAL STRUCTURE OF TUBULIN-STATHMIN-TTL-Vinblastine COMPLEX | ||||||
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![]() | STRUCTURAL PROTEIN / Complex | ||||||
Function / homology | ![]() tubulin-tyrosine ligase activity / microtubule depolymerization / 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 / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development ...tubulin-tyrosine ligase activity / microtubule depolymerization / 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 / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / mitotic cell cycle / growth cone / microtubule / neuron projection / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Wang, Y. / Chen, Q. / Zhang, R. | ||||||
![]() | ![]() Title: Structural Insights into the Pharmacophore of Vinca Domain Inhibitors of Microtubules. Authors: Wang, Y. / Benz, F.W. / Wu, Y. / Wang, Q. / Chen, Y. / Chen, X. / Li, H. / Zhang, Y. / Zhang, R. / 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 | ![]() | 463.6 KB | Display | ![]() |
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PDB format | ![]() | 367.9 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 | ![]() | 80.9 KB | Display | |
Data in CIF | ![]() | 108.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zhqC ![]() 4zi7C ![]() 4zolC ![]() 4tv8S S: Starting model for refinement C: citing same article ( |
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Similar 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
-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: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | | Mass: 16844.162 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 49-189 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 , 9 types, 241 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/VLB.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/GDP.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/VLB.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 | #10: Chemical | #11: Chemical | ChemComp-VLB / ( | #12: Chemical | ChemComp-ACP / | #13: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 6% PEG, 5% glycerol, 0.1M MES, 30 mM CaCl2, 30 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 106106 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 19 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4TV8 Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.35 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.423 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.68 Å2 / Biso mean: 53.32 Å2 / Biso min: 17.38 Å2
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Refinement step | Cycle: final / Resolution: 2.5→50 Å
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Refine LS restraints |
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