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Yorodumi- PDB-1e1x: HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR NU6027 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e1x | ||||||
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Title | HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR NU6027 | ||||||
Components | CYCLIN-DEPENDENT PROTEIN KINASE 2 | ||||||
Keywords | PROTEIN KINASE / CELL CYCLE / PHOSPHORYLATION / CELL DIVISION / MITOSIS / INHIBITION | ||||||
Function / homology | Function and homology information Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich ...Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Endicott, J.A. / Noble, M.E.M. / Johnson, L.N. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2000 Title: Identification of Novel Purine and Pyrimidine Cyclin-Dependent Kinase Inhibitors with Distinct Molecular Interactions and Tumor Cell Growth Inhibition Profiles. Authors: Arris, C.E. / Boyle, F.T. / Calvert, A.H. / Curtin, N.J. / Endicott, J.A. / Garman, E.F. / Gibson, A.E. / Golding, B.T. / Grant, S. / Griffin, R.J. / Jewsbury, P. / Johnson, L.N. / Lawrie, A. ...Authors: Arris, C.E. / Boyle, F.T. / Calvert, A.H. / Curtin, N.J. / Endicott, J.A. / Garman, E.F. / Gibson, A.E. / Golding, B.T. / Grant, S. / Griffin, R.J. / Jewsbury, P. / Johnson, L.N. / Lawrie, A.M. / Newell, D.R. / Noble, M.E.M. / Sausville, E.A. / Schultz, R. / Yu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e1x.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e1x.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 1e1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e1x_validation.pdf.gz | 448.1 KB | Display | wwPDB validaton report |
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Full document | 1e1x_full_validation.pdf.gz | 462.6 KB | Display | |
Data in XML | 1e1x_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 1e1x_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/1e1x ftp://data.pdbj.org/pub/pdb/validation_reports/e1/1e1x | HTTPS FTP |
-Related structure data
Related structure data | 1e1vC 1hckS 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: 34002.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COMPLEX WITH CYCLIN A OR CYCLIN E / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P24941, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-NW1 / |
#3: 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: 1.94 Å3/Da / Density % sol: 36.52 % |
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Crystal grow | Method: vapor diffusion / pH: 7.4 Details: PROTEIN AT 10MG/ML IN 15MM NACL, 10MM HEPES, PH7.4, MIXED WITH WELL BUFFER (50MM AMMONIUM ACETATE, 10% PEG4K, 0.1M HEPES PH 7.4) IN EQUAL VOLUMES, THEN VAPOUR DIFFUSION AGAINST WELL BUFFER. ...Details: PROTEIN AT 10MG/ML IN 15MM NACL, 10MM HEPES, PH7.4, MIXED WITH WELL BUFFER (50MM AMMONIUM ACETATE, 10% PEG4K, 0.1M HEPES PH 7.4) IN EQUAL VOLUMES, THEN VAPOUR DIFFUSION AGAINST WELL BUFFER. CDK2 CRYSTALS WERE SOAKED FOR 20 HOURS IN A SOLUTION OF 0.5MM NU2058 IN 1X WELL BUFFER PREPARED FROM STOCKS 2X WELLBUFFER AND 10MM NU6027 IN 100% DMSO. |
Crystal grow | *PLUS Method: other / Details: Lawrie, A.M., (1997) Nature Struct. Biol., 4, 796. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.94 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 22399 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.85→1.93 Å / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.27 / % possible all: 97.2 |
Reflection | *PLUS Num. measured all: 62274 |
Reflection shell | *PLUS % possible obs: 97.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HCK Resolution: 1.85→25 Å / σ(F): 0 Details: RESIDUES 36 - 43 WERE NOT MODELLED DUE TO POOR ELECTRON DENSITY.
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Refinement step | Cycle: LAST / Resolution: 1.85→25 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.213 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |