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Yorodumi- PDB-5zo7: Kinesin spindle protein Eg5 in complex with STLC-type inhibitor P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zo7 | ||||||
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Title | Kinesin spindle protein Eg5 in complex with STLC-type inhibitor PVEI0138 | ||||||
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: 2.6 Å | ||||||
Authors | Yokoyama, H. / Sato, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acs Omega / Year: 2018 Title: Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors. Authors: Yokoyama, H. / Sawada, J.I. / Sato, K. / Ogo, N. / Kamei, N. / Ishikawa, Y. / Hara, K. / Asai, A. / Hashimoto, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zo7.cif.gz | 287.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zo7.ent.gz | 230.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/5zo7 ftp://data.pdbj.org/pub/pdb/validation_reports/zo/5zo7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41300.910 Da / Num. of mol.: 2 / Fragment: Kinesin motor domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1, TRIP5 / Plasmid: pColdIII / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus RIL / References: UniProt: P52732 |
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-Non-polymers , 5 types, 81 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.22 Å3/Da / Density % sol: 44.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30% PEG 3350, 0.1M MES, 0.2M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 26, 2015 / Details: mirror |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 22457 / % possible obs: 99.2 % / Redundancy: 4.37 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.6→2.74 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 3209 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.52 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 34.494 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.397 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.706 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→19.52 Å
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Refine LS restraints |
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