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Yorodumi- PDB-2pg2: Crystal structure of KSP in complex with ADP and thiophene contai... -
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-Basic information
Entry | Database: PDB / ID: 2pg2 | ||||||
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Title | Crystal structure of KSP in complex with ADP and thiophene containing inhibitor 15 | ||||||
Components | Kinesin-like protein KIF11 | ||||||
Keywords | MOTOR PROTEIN / CELL CYCLE / kinesin spindle protein / KSP / Eg5 / complex / inhibitor / thiophene | ||||||
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: 1.849 Å | ||||||
Authors | Lee, T.T. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2007 Title: Synthesis and SAR of thiophene containing kinesin spindle protein (KSP) inhibitors Authors: Pinkerton, A.B. / Lee, T.T. / Hoffman, T.Z. / Wang, Y. / Kahraman, M. / Cook, T.G. / Severance, D. / Gahman, T.C. / Noble, S.A. / Shiau, A.K. / Davis, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pg2.cif.gz | 156.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pg2.ent.gz | 120.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/2pg2 ftp://data.pdbj.org/pub/pdb/validation_reports/pg/2pg2 | HTTPS FTP |
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-Related structure data
Related structure data | 2uyiC 2uymC 1q0bS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 41055.582 Da / Num. of mol.: 2 / Fragment: Catalytic domain (residues 1-368) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1, TRIP5 / Plasmid: PET30a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: 2.71 Å3/Da / Density % sol: 54.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM Bis-Tris (pH 6.0) 200 mM ammonium sulfate, and 18-20% PEG 3350. 10 mM SrCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.849→80.06 Å / Num. obs: 74875 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Q0B Resolution: 1.849→80.06 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.898 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.897 Å2
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Refinement step | Cycle: LAST / Resolution: 1.849→80.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.849→1.897 Å / Total num. of bins used: 20
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