+Open data
-Basic information
Entry | Database: PDB / ID: 5xag | ||||||
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Title | Crystal structure of tubulin-stathmin-TTL-Compound Z2 complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Tubulin | ||||||
Function / homology | Function and homology information tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / 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 / neuron projection development / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle / nervous system development / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Rattus norvegicus (Norway rat) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Zhang, H. / Luo, C. / Wang, Y. | ||||||
Citation | Journal: Eur J Med Chem / Year: 2017 Title: Design, synthesis, biological evaluation and cocrystal structures with tubulin of chiral beta-lactam bridged combretastatin A-4 analogues as potent antitumor agents Authors: Zhou, P. / Liang, Y. / Zhang, H. / Jiang, H. / Feng, K. / Xu, P. / Wang, J. / Wang, X. / Ding, K. / Luo, C. / Liu, M. / Wang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xag.cif.gz | 461.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xag.ent.gz | 365.6 KB | Display | PDB format |
PDBx/mmJSON format | 5xag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/5xag ftp://data.pdbj.org/pub/pdb/validation_reports/xa/5xag | HTTPS FTP |
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-Related structure data
Related structure data | 5xafC 4o2bS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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: 50204.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Bos taurus (cattle) / References: UniProt: P81947 #2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: TUBB2B / Production host: Bos taurus (cattle) / References: UniProt: Q6B856 #3: Protein | | Mass: 22125.301 Da / Num. of mol.: 1 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: 43549.625 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 , 10 types, 161 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-GOL / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-MES / | #11: Chemical | #12: Chemical | #13: Chemical | ChemComp-ACP / | #14: 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: 2.75 Å3/Da / Density % sol: 55.31 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 6% PEG 4000, 8% glycerol, 100mM 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: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.555→47.918 Å / Num. obs: 96811 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 14.45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O2B Resolution: 2.56→47.92 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.85 / 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: 2.56→47.92 Å
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Refine LS restraints |
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LS refinement shell |
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