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Yorodumi- PDB-5xlt: The crystal structure of tubulin in complex with 4'-demethylepipo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xlt | ||||||
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Title | The crystal structure of tubulin in complex with 4'-demethylepipodophyllotoxin | ||||||
Components |
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Keywords | CELL CYCLE / tubulin / inhibitor | ||||||
Function / homology | Function and homology information tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / nervous system development / growth cone / microtubule / neuron projection / protein heterodimerization activity / GTPase activity / nucleotide binding / GTP binding / Golgi apparatus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Gallus gallus (chicken) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.813 Å | ||||||
Authors | Yu, Y. / Chen, Q. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Structure of 4'-demethylepipodophyllotoxin in complex with tubulin provides a rationale for drug design Authors: Niu, L. / Wang, Y. / Wang, C. / Wang, Y. / Jiang, X. / Ma, L. / Wu, C. / Yu, Y. / Chen, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xlt.cif.gz | 819.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xlt.ent.gz | 675.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xlt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xlt_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 5xlt_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 5xlt_validation.xml.gz | 75.2 KB | Display | |
Data in CIF | 5xlt_validation.cif.gz | 99.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/5xlt ftp://data.pdbj.org/pub/pdb/validation_reports/xl/5xlt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-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: 50041.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947 #2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856 #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.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043 #4: Protein | | Mass: 44378.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43 |
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-Non-polymers , 8 types, 108 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-ACP / | #12: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 6% poly(ethylene glycol) 4000, 8% glycerol, 0.1M Mes, 30mM CaCl2, 30mM MgCl2 (pH 6.7) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 72745 / % possible obs: 99.9 % / Redundancy: 6.7 % / Net I/σ(I): 11.5 |
-Processing
Software |
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Refinement | Resolution: 2.813→46.862 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.38 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.813→46.862 Å
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Refine LS restraints |
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LS refinement shell |
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