+Open data
-Basic information
Entry | Database: PDB / ID: 5yl4 | ||||||
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Title | CRYSTAL STRUCTURE OF T2R-TTL-8WR COMPLEX | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / TUBULIN / MICROTUBULE / COLCHICINE / DIKETOPIPERAZINE | ||||||
Function / homology | Function and homology information tubulin-tyrosine ligase activity / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / mitotic cell cycle ...tubulin-tyrosine ligase activity / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / mitotic cell cycle / growth cone / microtubule / hydrolase activity / neuron projection / GTPase activity / nucleotide binding / GTP binding / Golgi apparatus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Gallus gallus (chicken) Sus barbatus (bearded pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.64 Å | ||||||
Authors | Fu, Z.Y. / Li, W.B. / Chu, Y.Y. / Hou, Y.W. / Ji, C.P. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Design, synthesis and biological activity evaluation of plinabulin derivatives based on co-crystal structure Authors: Fu, Z.Y. / Li, W.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yl4.cif.gz | 449.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yl4.ent.gz | 357.6 KB | Display | PDB format |
PDBx/mmJSON format | 5yl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yl4_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 5yl4_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 5yl4_validation.xml.gz | 73.1 KB | Display | |
Data in CIF | 5yl4_validation.cif.gz | 100.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/5yl4 ftp://data.pdbj.org/pub/pdb/validation_reports/yl/5yl4 | HTTPS FTP |
-Related structure data
Related structure data | |
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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) Sus barbatus (bearded pig) / References: UniProt: A0A0R4I993 #2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus barbatus (bearded pig) / References: UniProt: A0A0R4I995 #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, 153 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | #8: Chemical | ChemComp-GDP / | #9: Chemical | #10: Chemical | ChemComp-8WR / ( | #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: 2.9 Å3/Da / Density % sol: 57.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 6% POLYETHYLENE GLYCOL 4000, 8% GLYCEROL, 0.1M MES, 30MM CACL2, 30MM MGCL2, PH 6.7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.594→50 Å / Num. obs: 93390 / % possible obs: 99.8 % / Redundancy: 4.2 % / Net I/σ(I): 11.6 |
-Processing
Software |
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Refinement | Resolution: 2.64→48.225 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.897 / SU B: 11.978 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.683 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.897 Å2
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Refinement step | Cycle: LAST / Resolution: 2.64→48.225 Å
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