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Yorodumi- PDB-4a51: Crystal structure of human kinesin Eg5 in complex with 1-(3-(((2-... -
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-Basic information
Entry | Database: PDB / ID: 4a51 | ||||||
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Title | Crystal structure of human kinesin Eg5 in complex with 1-(3-(((2-Aminoethyl)thio)diphenylmethyl)phenyl)ethanone hydrochloride | ||||||
Components | KINESIN-LIKE PROTEIN KIF11 | ||||||
Keywords | CELL CYCLE / MITOSIS / INHIBITOR / 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: 2.75 Å | ||||||
Authors | Kaan, H.Y.K. / Kozielski, F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Triphenylbutanamines: Kinesin Spindle Protein Inhibitors with in Vivo Antitumor Activity. Authors: Wang, F. / Good, J.A.D. / Rath, O. / Kaan, H.Y.K. / Sutcliffe, O.B. / Mackay, S.P. / Kozielski, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a51.cif.gz | 461.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a51.ent.gz | 376.6 KB | Display | PDB format |
PDBx/mmJSON format | 4a51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/4a51 ftp://data.pdbj.org/pub/pdb/validation_reports/a5/4a51 | HTTPS FTP |
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-Related structure data
Related structure data | 4a50C 1x88S 4a2t 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
-Protein , 1 types, 7 molecules ABCDEFG
#1: Protein | Mass: 41055.582 Da / Num. of mol.: 7 / 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, 261 molecules
#2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-DQ8 / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-SO4 / | #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: 3.37 Å3/Da / Density % sol: 63.53 % / Description: NONE |
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Crystal grow | pH: 5.8 Details: 22 % POLYETHYLENE GLYCOL-3350, 0.25 M AMMONIUM SULPHATE, 0.1 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE AND 0.1 M MES PH 5.8 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.636 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.636 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. obs: 98930 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 58.62 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.7 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1X88 Resolution: 2.75→29.991 Å / SU ML: 0.78 / σ(F): 1.35 / Phase error: 29.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.454 Å2 / ksol: 0.345 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→29.991 Å
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Refine LS restraints |
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LS refinement shell |
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