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- PDB-3dbe: Crystal structure of an activated (Thr->Asp) Polo-like kinase 1 (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dbe | ||||||
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Title | Crystal structure of an activated (Thr->Asp) Polo-like kinase 1 (Plk1) catalytic domain in complex with Compound 557 | ||||||
![]() | Polo-like kinase 1 | ||||||
![]() | TRANSFERASE / Polo-like kinase 1 / Plk1 / catalytic domain / small-molecule inhibitor / Kinase | ||||||
Function / homology | ![]() Polo-like kinase mediated events / Phosphorylation of Emi1 / Condensation of Prophase Chromosomes / Resolution of Sister Chromatid Cohesion / Mitotic Metaphase/Anaphase Transition / Mitotic Telophase/Cytokinesis / Cyclin A/B1/B2 associated events during G2/M transition / EML4 and NUDC in mitotic spindle formation / Regulation of PLK1 Activity at G2/M Transition / The role of GTSE1 in G2/M progression after G2 checkpoint ...Polo-like kinase mediated events / Phosphorylation of Emi1 / Condensation of Prophase Chromosomes / Resolution of Sister Chromatid Cohesion / Mitotic Metaphase/Anaphase Transition / Mitotic Telophase/Cytokinesis / Cyclin A/B1/B2 associated events during G2/M transition / EML4 and NUDC in mitotic spindle formation / Regulation of PLK1 Activity at G2/M Transition / The role of GTSE1 in G2/M progression after G2 checkpoint / polo kinase / mitotic spindle organization / kinetochore / spindle pole / retina development in camera-type eye / mitotic cell cycle / cell division / protein serine/threonine kinase activity / centrosome / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Elling, R.A. / Barr, K.J. / Romanowski, M.J. | ||||||
![]() | ![]() Title: Design and synthesis of 2-amino-pyrazolopyridines as Polo-like kinase 1 inhibitors. Authors: Fucini, R.V. / Hanan, E.J. / Romanowski, M.J. / Elling, R.A. / Lew, W. / Barr, K.J. / Zhu, J. / Yoburn, J.C. / Liu, Y. / Fahr, B.T. / Fan, J. / Lu, Y. / Pham, P. / Choong, I.C. / ...Authors: Fucini, R.V. / Hanan, E.J. / Romanowski, M.J. / Elling, R.A. / Lew, W. / Barr, K.J. / Zhu, J. / Yoburn, J.C. / Liu, Y. / Fahr, B.T. / Fan, J. / Lu, Y. / Pham, P. / Choong, I.C. / VanderPorten, E.C. / Bui, M. / Purkey, H.E. / Evanchik, M.J. / Yang, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 72.3 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3dbcC ![]() 3dbdC ![]() 3dbfC ![]() 3d5wS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34442.113 Da / Num. of mol.: 1 / Fragment: Plk1 kinase domain / Mutation: T196D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-4FR / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: hanging-drop vapor diffusion at 4 C (277K); protein at 7 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl and 3 mM DTT; crystallization condition: 0.1 M HEPES pH 7.5, 0.2 M (NH4)2SO4, 22.5% PEG ...Details: hanging-drop vapor diffusion at 4 C (277K); protein at 7 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl and 3 mM DTT; crystallization condition: 0.1 M HEPES pH 7.5, 0.2 M (NH4)2SO4, 22.5% PEG 3350, and 15% glycerol; cryoprotectant: 15% ethylene glycol., VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 160 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2007 |
Radiation | Monochromator: Side-scattering cube root I-beam bent single crystal; asymmetric cut 12.2 degs. Crystal type: Si(311) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.32→30 Å / Num. obs: 6290 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 3.32→3.5 Å / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3d5w Resolution: 3.32→30 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.879 / SU B: 32.49 / SU ML: 0.514 / Cross valid method: THROUGHOUT / ESU R Free: 0.608 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.32→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.32→3.435 Å / Total num. of bins used: 15
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