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- PDB-1dm2: HUMAN CYCLIN-DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR HYME... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dm2 | ||||||
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Title | HUMAN CYCLIN-DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR HYMENIALDISINE | ||||||
![]() | CYCLIN-DEPENDENT KINASE 2![]() | ||||||
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Function / homology | ![]() cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Thunnissen, A.M. / Kim, S.-H. | ||||||
![]() | ![]() Title: Inhibition of cyclin-dependent kinases, GSK-3beta and CK1 by hymenialdisine, a marine sponge constituent. Authors: Meijer, L. / Thunnissen, A.M. / White, A.W. / Garnier, M. / Nikolic, M. / Tsai, L.H. / Walter, J. / Cleverley, K.E. / Salinas, P.C. / Wu, Y.Z. / Biernat, J. / Mandelkow, E.M. / Kim, S.H. / Pettit, G.R. #1: ![]() Title: Exploiting Chemical Libraries, Structure, and Genomics in the Search for Kinase Inhibitors Authors: Gray, N.S. / Wodicka, L. / Thunnissen, A.M.W.H. / Norman, T.C. / Kwon, S. / Espinoza, F.H. / Morgan, D.O. / Barnes, G. / Leclerc, S. / Meijer, L. / Kim, S.-H. / Lockhart, D.J. / Schultz, P.G. #2: ![]() Title: Inhibition of Cyclin-Dependent Kinases by Purine Analogues-Crystal Structure of Human Cdk2 Complexed with Roscovitine Authors: De Azevedo, W.F. / Leclerc, S. / Meijer, L. / Havlicek, L. / Strnad, M. / Kim, S.-H. #3: ![]() Title: Multiple Modes of Ligand Recognition: Crystal Structures of Cyclin-Dependent Protein Kinase 2 in Complex with ATP and Two Inhibitors, Olomoucine and Isopentenyladenine Authors: Schultze-Gahmen, U. / Brandsen, J. / Jones, H.D. / Morgan, D.O. / Meijer, L. / Vesely, J. / Kim, S.-H. #4: ![]() Title: Crystal Structure of Cyclin-Dependent Kinase 2 Authors: De Bondt, H.L. / Rosenblatt, J. / Jancarik, J. / Jones, H.D. / Morgan, D.O. / Kim, S.-H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.2 KB | Display | ![]() |
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PDB format | ![]() | 52.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | ![]() Mass: 33976.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P24941, ![]() | ||
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#2: Chemical | ChemComp-HMD / | ||
#3: Chemical | ChemComp-EDO / ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: HEPES, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 278K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion / Details: Rosenblatt, J., (1993) J. Mol. Biol., 230, 1317. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 5, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→30 Å / Num. all: 51723 / Num. obs: 16264 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.223 / % possible all: 86.6 |
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Processing
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Refinement | Resolution: 2.1→30 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 34.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å / σ(F): 1 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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