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Yorodumi- PDB-3wpn: Kinesin spindle protein Eg5 in complex with ATP-competitive inhib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wpn | ||||||
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Title | Kinesin spindle protein Eg5 in complex with ATP-competitive inhibitor PVZB1194 | ||||||
Components | Kinesin-like protein KIF11 | ||||||
Keywords | CELL CYCLE / motor domain / ATP binding | ||||||
Function / homology | Function and homology information spindle elongation / Kinesins / plus-end-directed microtubule motor activity / regulation of mitotic centrosome separation / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement ...spindle elongation / Kinesins / plus-end-directed microtubule motor activity / regulation of mitotic centrosome separation / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / mitotic spindle / spindle / spindle pole / mitotic cell cycle / microtubule binding / microtubule / cell division / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Yokoyama, H. / Katoh, S. / Fujii, S. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2015 Title: Structural basis of new allosteric inhibition in Kinesin spindle protein eg5 Authors: Yokoyama, H. / Sawada, J. / Katoh, S. / Matsuno, K. / Ogo, N. / Ishikawa, Y. / Hashimoto, H. / Fujii, S. / Asai, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wpn.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wpn.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 3wpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/3wpn ftp://data.pdbj.org/pub/pdb/validation_reports/wp/3wpn | HTTPS FTP |
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-Related structure data
Related structure data | 1q0bS 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
#1: Protein | Mass: 42875.633 Da / Num. of mol.: 1 / Fragment: motor domain, residues 1-369 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EG5, KIF11 / Plasmid: pColdIII / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P52732 |
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#2: Chemical | ChemComp-B4S / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 19% PEG3350, 0.1M MES, 0.2M NaNO3, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2012 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 10303 / % possible obs: 98.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 65.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 38.7 |
Reflection shell | Resolution: 2.8→2.85 Å / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 6.8 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q0B Resolution: 2.8→19.88 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.873 / SU B: 14.955 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.804 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.88 Å
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