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Yorodumi- PDB-5gon: Structures of a beta-lactam bridged analogue in complex with tubulin -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gon | ||||||
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Title | Structures of a beta-lactam bridged analogue in complex with tubulin | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / beta-lactam bridged analogue tubulin colchicine binding site | ||||||
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 | Gallus gallus (chicken) Bos taurus (cattle) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.48 Å | ||||||
Authors | Zhou, L. / Liu, Y. / Cheng, L. / Wang, Y. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2016 Title: Potent Antitumor Activities and Structure Basis of the Chiral beta-Lactam Bridged Analogue of Combretastatin A-4 Binding to Tubulin. Authors: Zhou, P. / Liu, Y. / Zhou, L. / Zhu, K. / Feng, K. / Zhang, H. / Liang, Y. / Jiang, H. / 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 | 5gon.cif.gz | 461.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gon.ent.gz | 368.5 KB | Display | PDB format |
PDBx/mmJSON format | 5gon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/5gon ftp://data.pdbj.org/pub/pdb/validation_reports/go/5gon | HTTPS FTP |
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-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: 48966.324 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-440 / 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 1-431 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856 #3: Protein | | Mass: 16082.335 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 50-185 / 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 genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: E1BQ43 |
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-Non-polymers , 9 types, 296 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-GOL / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-MES / | #11: Chemical | ChemComp-6ZR / ( | #12: Chemical | #13: Water | ChemComp-HOH / | |
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-Details
Sequence details | IN CHAINS B AND D, RESIDUE NUMBERS 43,44, 361-368 ARE SIMPLY SKIPPED. |
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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: 3.04 Å3/Da / Density % sol: 59.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 6% polyethylene glycol 4000, 8% glycerol, 0.1 M MES, 30 mM CaCl2, 30 mM MgCl2, pH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97845 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97845 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→118.6 Å / Num. obs: 98970 / % possible obs: 92.9 % / Redundancy: 4.5 % / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.48→2.57 Å |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→118.6 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.892 / SU B: 9.543 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.47 / ESU R Free: 0.289 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.82 Å2
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Refinement step | Cycle: LAST / Resolution: 2.48→118.6 Å
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