+Open data
-Basic information
Entry | Database: PDB / ID: 7z7d | ||||||||||||
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Title | Tubulin-Todalam-Vinblastine-complex | ||||||||||||
Components |
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Keywords | CELL CYCLE / TUBULIN FOLD / CYTOSKELETON / MICROTUBULE | ||||||||||||
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 / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||||||||
Authors | Muehlethaler, T. / Milanos, L. / Ortega, J.A. / Blum, T.B. / Gioia, D. / Roy, B. / Prota, A.E. / Cavalli, A. / Steinmetz, M.O. | ||||||||||||
Funding support | European Union, Switzerland, 3items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022 Title: Rational Design of a Novel Tubulin Inhibitor with a Unique Mechanism of Action. Authors: Muhlethaler, T. / Milanos, L. / Ortega, J.A. / Blum, T.B. / Gioia, D. / Roy, B. / Prota, A.E. / Cavalli, A. / Steinmetz, M.O. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z7d.cif.gz | 480.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z7d.ent.gz | 379.6 KB | Display | PDB format |
PDBx/mmJSON format | 7z7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/7z7d ftp://data.pdbj.org/pub/pdb/validation_reports/z7/7z7d | HTTPS FTP |
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-Related structure data
Related structure data | 5sb3C 5sb4C 5sb5C 5sb6C 5sb7C 5lxtS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 3 molecules ACE
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: P81947 #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 |
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-Tubulin beta-2B ... , 2 types, 3 molecules BDF
#2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: Q6B856 #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 , 9 types, 873 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-CA / #8: Chemical | #9: Chemical | ChemComp-MES / | #10: Chemical | ChemComp-VLB / ( | #11: Chemical | ChemComp-4I2 / | #12: Chemical | ChemComp-ACP / | #13: 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: 2.8 Å3/Da / Density % sol: 56.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2% PEG 4K, 4% glycerol, 30 mM MgCl2, 30 mM CaCl2, 0.1 M MES/Imidazole, 5 mM L-tyrosine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.6 Å / Num. obs: 405947 / % possible obs: 96.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 40.97 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.07222 / Rpim(I) all: 0.03566 / Rrim(I) all: 0.08104 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2→2.08 Å / Rmerge(I) obs: 1.274 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 64331 / CC1/2: 0.386 / CC star: 0.746 / Rpim(I) all: 0.6473 / Rrim(I) all: 1.437 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5lxt Resolution: 2→45.6 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.34 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.8 Å2 / Biso mean: 54.6883 Å2 / Biso min: 19.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→45.6 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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