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Yorodumi- PDB-2x7c: Crystal structure of human kinesin Eg5 in complex with (S)-enastron -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x7c | ||||||
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Title | Crystal structure of human kinesin Eg5 in complex with (S)-enastron | ||||||
Components | KINESIN-LIKE PROTEIN KIF11 | ||||||
Keywords | CELL CYCLE / MICROTUBULE / ATP-BINDING / MOTOR PROTEIN / CELL DIVISION / MITOSIS / INHIBITOR / NUCLEOTIDE-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: 1.9 Å | ||||||
Authors | Kaan, H.Y.K. / Ulaganathan, V. / Rath, O. / Laggner, C. / Prokopcova, H. / Dallinger, D. / Kappe, C.O. / Kozielski, F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 Title: Structural Basis for Inhibition of Eg5 by Dihydropyrimidines: Stereoselectivity of Antimitotic Inhibitors Enastron, Dimethylenastron and Fluorastrol. Authors: Kaan, H.Y.K. / Ulaganathan, V. / Rath, O. / Prokopcova, H. / Dallinger, D. / Kappe, C.O. / Kozielski, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x7c.cif.gz | 315.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x7c.ent.gz | 254 KB | Display | PDB format |
PDBx/mmJSON format | 2x7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/2x7c ftp://data.pdbj.org/pub/pdb/validation_reports/x7/2x7c | HTTPS FTP |
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-Related structure data
Related structure data | 2x7dC 2x7eC 1x88S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41055.582 Da / Num. of mol.: 2 / Fragment: MOTOR DOMAIN, RESIDUES 1-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLYSS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P52732 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.76 Å3/Da / Density % sol: 55.54 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 25% PEG3350, 0.2M K2HPO4, 0.1M HEPES PH8.0 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.076 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.076 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 69235 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.9 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X88 Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.346 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: 19.835 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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