+Open data
-Basic information
Entry | Database: PDB / ID: 5z4p | |||||||||
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Title | Crystal structure of tubulin-stathmin-TTL-Compound TCA complex | |||||||||
Components |
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Keywords | OXYGEN TRANSPORT / Tubulin | |||||||||
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 / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / 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: 2.5 Å | |||||||||
Authors | Zhang, H. / Luo, C. | |||||||||
Citation | Journal: To Be Published Title: Discovery and Design of novel Tubulin inhibitors Authors: Zhang, H. / Luo, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z4p.cif.gz | 453.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z4p.ent.gz | 358.7 KB | Display | PDB format |
PDBx/mmJSON format | 5z4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z4p_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 5z4p_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 5z4p_validation.xml.gz | 84 KB | Display | |
Data in CIF | 5z4p_validation.cif.gz | 110.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/5z4p ftp://data.pdbj.org/pub/pdb/validation_reports/z4/5z4p | HTTPS FTP |
-Related structure data
Related structure data | 4o2bS 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: 48966.324 Da / Num. of mol.: 2 / Fragment: UNP residues 1-438 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947 #2: Protein | Mass: 48391.410 Da / Num. of mol.: 2 / Fragment: UNP residues 1-425 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856 #3: Protein | | Mass: 21680.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P63043 #4: Protein | | Mass: 43549.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: E1BQ43 |
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-Non-polymers , 10 types, 80 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-GOL / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-MES / | #11: Chemical | ChemComp-97O / | #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: 2.77 Å3/Da / Density % sol: 55.52 % |
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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 PILATUS3 S 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: 2.5→49.64 Å / Num. obs: 101936 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 9.88 |
Reflection shell | Resolution: 2.5→2.665 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O2B Resolution: 2.5→49.636 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.18 / 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: 2.5→49.636 Å
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Refine LS restraints |
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LS refinement shell |
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