+Open data
-Basic information
Entry | Database: PDB / ID: 6knz | ||||||
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Title | Crystal structure of T2R-TTL-KXO1 complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Tubulin / Inhibitor / Complex | ||||||
Function / homology | Function and homology information tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spindle microtubule / protein modification process / structural constituent of cytoskeleton ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / mitotic cell cycle / nervous system development / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Gallus gallus (chicken) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.475 Å | ||||||
Authors | Chen, Q. / Yu, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Reversible binding of the anticancer drug KXO1 (tirbanibulin) to the colchicine-binding site of beta-tubulin explains KXO1's low clinical toxicity. Authors: Niu, L. / Yang, J. / Yan, W. / Yu, Y. / Zheng, Y. / Ye, H. / Chen, Q. / Chen, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6knz.cif.gz | 835.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6knz.ent.gz | 687.5 KB | Display | PDB format |
PDBx/mmJSON format | 6knz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/6knz ftp://data.pdbj.org/pub/pdb/validation_reports/kn/6knz | HTTPS FTP |
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-Related structure data
Related structure data | 5iyzS 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: 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 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, 242 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-CA / #8: Chemical | ChemComp-GDP / | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-ACP / | #12: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.87 Å3/Da / Density % sol: 57.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 6% poly(ethylene glycol) 4000, 8% glycerol, 0.1 M MES (pH 6.7), 30 mM CaCl2, 30 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97777 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97777 Å / Relative weight: 1 |
Reflection | Resolution: 2.475→50 Å / Num. obs: 106839 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.995 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.475→2.54 Å / Num. unique obs: 5268 / CC1/2: 0.812 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IYZ Resolution: 2.475→26.232 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 335.22 Å2 / Biso mean: 73.8185 Å2 / Biso min: 23.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.475→26.232 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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