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Yorodumi- PDB-2x7d: Crystal structure of human kinesin Eg5 in complex with (S)-dimeth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x7d | ||||||
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Title | Crystal structure of human kinesin Eg5 in complex with (S)-dimethylenastron | ||||||
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 / regulation of mitotic centrosome separation / Kinesins / plus-end-directed microtubule motor activity / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / spindle organization / microtubule-based movement ...spindle elongation / regulation of mitotic centrosome separation / Kinesins / plus-end-directed microtubule motor activity / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / spindle organization / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / mitotic spindle / spindle pole / spindle / 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: 2.3 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 | 2x7d.cif.gz | 163.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x7d.ent.gz | 127.1 KB | Display | PDB format |
PDBx/mmJSON format | 2x7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x7d_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2x7d_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2x7d_validation.xml.gz | 34.7 KB | Display | |
Data in CIF | 2x7d_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/2x7d ftp://data.pdbj.org/pub/pdb/validation_reports/x7/2x7d | HTTPS FTP |
-Related structure data
Related structure data | 2x7cC 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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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 | ChemComp-MG / #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: 2.69 Å3/Da / Density % sol: 54.32 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 30% PEG 3350, 0.2M K2HPO4, 0.1M HEPES PH 8.0 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.92 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 40030 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.3→2.43 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.5 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X88 Resolution: 2.3→29.58 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.506 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.224 / 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: 21.346 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→29.58 Å
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