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Yorodumi- PDB-2gm1: Crystal structure of the mitotic kinesin eg5 in complex with mg-a... -
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-Basic information
Entry | Database: PDB / ID: 2gm1 | ||||||
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Title | Crystal structure of the mitotic kinesin eg5 in complex with mg-adp and n-(3-aminopropyl)-n-((3-benzyl-5-chloro-4-oxo-3,4-dihydropyrrolo[2,1-f][1,2,4]triazin-2-yl)(cyclopropyl)methyl)-4-methylbenzamide | ||||||
Components | KINESIN-RELATED MOTOR PROTEIN EG5 | ||||||
Keywords | CELL CYCLE / Eg5 Mg-ADP Complex 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: 2.3 Å | ||||||
Authors | Sheriff, S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Synthesis and SAR of pyrrolotriazine-4-one based Eg5 inhibitors. Authors: Kim, K.S. / Lu, S. / Cornelius, L.A. / Lombardo, L.J. / Borzilleri, R.M. / Schroeder, G.M. / Sheng, C. / Rovnyak, G. / Crews, D. / Schmidt, R.J. / Williams, D.K. / Bhide, R.S. / Traeger, S.C. ...Authors: Kim, K.S. / Lu, S. / Cornelius, L.A. / Lombardo, L.J. / Borzilleri, R.M. / Schroeder, G.M. / Sheng, C. / Rovnyak, G. / Crews, D. / Schmidt, R.J. / Williams, D.K. / Bhide, R.S. / Traeger, S.C. / McDonnell, P.A. / Mueller, L. / Sheriff, S. / Newitt, J.A. / Pudzianowski, A.T. / Yang, Z. / Wild, R. / Lee, F.Y. / Batorsky, R. / Ryder, J.S. / Ortega-Nanos, M. / Shen, H. / Gottardis, M. / Roussell, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gm1.cif.gz | 272.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gm1.ent.gz | 217.1 KB | Display | PDB format |
PDBx/mmJSON format | 2gm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/2gm1 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/2gm1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 41055.582 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EG5 / Plasmid: PET 43D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P52732 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-2AZ / #4: Chemical | ChemComp-ADP / #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: 2.4 Å3/Da / Density % sol: 48.69 % |
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Crystal grow | Temperature: 277 K / pH: 7.5 Details: 1:1 reservoir: 0.1 M NaHEPES pH 7.5, 0.2 M MgCl2, 28% (v/v) PEG-3350; protein: 3.69 mg/ml (90 uM) in 20 mM PIPES pH 6.8, 2 mM MgCl2, 1 mM EGTA, 25 mM DTT, 478 uM ADP, 478 uM BMS-607205, 1.0% ...Details: 1:1 reservoir: 0.1 M NaHEPES pH 7.5, 0.2 M MgCl2, 28% (v/v) PEG-3350; protein: 3.69 mg/ml (90 uM) in 20 mM PIPES pH 6.8, 2 mM MgCl2, 1 mM EGTA, 25 mM DTT, 478 uM ADP, 478 uM BMS-607205, 1.0% DMSO , pH 7.8, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC / Detector: CCD / Date: Jun 26, 2003 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.8 % / Av σ(I) over netI: 11.4 / Number: 254796 / Rmerge(I) obs: 0.067 / Χ2: 1.04 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 67500 / % possible obs: 99.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell | ID: 1
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Reflection | Resolution: 2.3→50 Å / Num. obs: 67500 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 5.1 / % possible all: 99.1 |
-Phasing
Phasing MR | Rfactor: 0.384 / Cor.coef. Fo:Fc: 0.652 / Cor.coef. Io to Ic: 0.682
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-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: EG5 TETRAMER Resolution: 2.3→49.86 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1956724.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Due to a feature in the refinement program, the structure was refined with an OXT on a residue that is not the terminal residue of the sequence. The OXT was changed to N of the next residue ...Details: Due to a feature in the refinement program, the structure was refined with an OXT on a residue that is not the terminal residue of the sequence. The OXT was changed to N of the next residue by the wwPDB annotation staff.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.409 Å2 / ksol: 0.369911 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→49.86 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
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Xplor file |
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