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Yorodumi- PDB-2xae: Crystal structure of human kinesin Eg5 in complex with (R)-2-amin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xae | ||||||
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Title | Crystal structure of human kinesin Eg5 in complex with (R)-2-amino-3-((S)-2-methyl-1,1-diphenylbutylthio)propanoic acid | ||||||
Components | KINESIN-LIKE PROTEIN KIF11 | ||||||
Keywords | CELL CYCLE / MITOSIS / KSP | ||||||
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 | Kaan, H.Y.K. / Weiss, J. / Menger, D. / Ulaganathan, V. / Tkocz, K. / Laggner, C. / Popowycz, F. / Joseph, B. / Kozielski, F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Structure-Activity Relationship and Multidrug Resistance Study of New S-Trityl-L-Cysteine Derivatives as Inhibitors of Eg5. Authors: Kaan, H.Y.K. / Weiss, J. / Menger, D. / Ulaganathan, V. / Tkocz, K. / Laggner, C. / Popowycz, F. / Joseph, B. / Kozielski, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xae.cif.gz | 220.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xae.ent.gz | 175.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/2xae ftp://data.pdbj.org/pub/pdb/validation_reports/xa/2xae | HTTPS FTP |
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-Related structure data
Related structure data | 2x2rC 2wogS 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 41055.582 Da / Num. of mol.: 3 / Fragment: MOTOR DOMAIN, RESIDUES 1-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P52732 |
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-Non-polymers , 6 types, 379 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | #7: 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: 2.74 Å3/Da / Density % sol: 55.17 % / Description: NONE |
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Crystal grow | pH: 6 Details: 24% POLYETHYLENE GLYCOL-3350, 0.25 M AMMONIUM SULPHATE, 0.01 M TRIMETHYLAMINE HYDROCHLORIDE AND 0.1 M MES PH 6.0 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 40212 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 57.22 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.8 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WOG Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.894 / SU B: 9.596 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.627 / ESU R Free: 0.318 / 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: 40.505 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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