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Yorodumi- PDB-4a50: Crystal structure of human kinesin Eg5 in complex with 2-Amino-5-... -
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-Basic information
Entry | Database: PDB / ID: 4a50 | ||||||
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Title | Crystal structure of human kinesin Eg5 in complex with 2-Amino-5-(3-methylphenyl)-5,5-diphenylpentanoic acid | ||||||
Components | KINESIN-LIKE PROTEIN KIF11 | ||||||
Keywords | CELL CYCLE / MITOSIS / INHIBITOR / KSP | ||||||
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: 2.75 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 | 4a50.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a50.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 4a50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a50_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4a50_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4a50_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 4a50_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/4a50 ftp://data.pdbj.org/pub/pdb/validation_reports/a5/4a50 | HTTPS FTP |
-Related structure data
Related structure data | 4a51C 3kenS 4a2t C: citing same article (ref.) S: Starting model for refinement |
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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, 1 molecules A
#1: Protein | Mass: 41055.582 Da / Num. of mol.: 1 / 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 , 5 types, 42 molecules
#2: Chemical | ChemComp-ADP / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-DQ6 / ( |
#5: Chemical | ChemComp-DQ7 / ( |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.69 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 23 % POLYETHYLENE GLYCOL-3350, 0.25 M AMMONIUM SULPHATE AND 0.1 M MES PH 5.5 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. obs: 17322 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KEN Resolution: 2.75→28.03 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.256 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.278 / 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: 65.825 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→28.03 Å
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