+Open data
-Basic information
Entry | Database: PDB / ID: 6g6y | ||||||
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Title | Eg5-inhibitor complex | ||||||
Components | Kinesin-like protein KIF11 | ||||||
Keywords | CELL CYCLE / Eg5 / Kif11 / Eg5-inhibitor | ||||||
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: 1.8 Å | ||||||
Authors | Talapatra, S.K. / Kozielski, F. / Tham, C.L. | ||||||
Citation | Journal: Eur J Med Chem / Year: 2018 Title: Crystal structure of the Eg5 - K858 complex and implications for structure-based design of thiadiazole-containing inhibitors. Authors: Talapatra, S.K. / Tham, C.L. / Guglielmi, P. / Cirilli, R. / Chandrasekaran, B. / Karpoormath, R. / Carradori, S. / Kozielski, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g6y.cif.gz | 86.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g6y.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 6g6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/6g6y ftp://data.pdbj.org/pub/pdb/validation_reports/g6/6g6y | HTTPS FTP |
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-Related structure data
Related structure data | 6g6zC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41209.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1, TRIP5 / Production host: Escherichia coli (E. coli) / References: UniProt: P52732 |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-EOK / (~{ |
#5: 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: 2.42 Å3/Da / Density % sol: 49.14 % / Description: Plate like single crystal |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M HEPES pH 8.0, 12.5 % PEG3350, and 0.1 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 33982 / % possible obs: 96.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3262 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1X88 Resolution: 1.8→48.72 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→48.72 Å
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Refine LS restraints |
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LS refinement shell |
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