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Yorodumi- PDB-1fvt: THE STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2) IN COMPLEX WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fvt | |||||||||
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Title | THE STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2) IN COMPLEX WITH AN OXINDOLE INHIBITOR | |||||||||
Components | CELL DIVISION PROTEIN KINASE 2 | |||||||||
Keywords | TRANSFERASE / CELL CYCLE / cyclin-dependent kinase / oxindole | |||||||||
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 / Resolution: 2.2 Å | |||||||||
Authors | Davis, S.T. / Benson, B.G. / Bramson, H.N. / Chapman, D.E. / Dickerson, S.H. / Dold, K.M. / Eberwein, D.J. / Edelstein, M. / Frye, S.V. / Gampe Jr., R.T. ...Davis, S.T. / Benson, B.G. / Bramson, H.N. / Chapman, D.E. / Dickerson, S.H. / Dold, K.M. / Eberwein, D.J. / Edelstein, M. / Frye, S.V. / Gampe Jr., R.T. / Griffin, R.J. / Harris, P.A. / Hassell, A.M. / Holmes, W.D. / Hunter, R.N. / Knick, V.B. / Lackey, K. / Lovejoy, B. / Luzzio, M.J. / Murray, D. / Parker, P. / Rocque, W.J. / Shewchuk, L. / Veal, J.M. / Walker, D.H. / Kuyper, L.K. | |||||||||
Citation | Journal: Science / Year: 2001 Title: Prevention of chemotherapy-induced alopecia in rats by CDK inhibitors. Authors: Davis, S.T. / Benson, B.G. / Bramson, H.N. / Chapman, D.E. / Dickerson, S.H. / Dold, K.M. / Eberwein, D.J. / Edelstein, M. / Frye, S.V. / Gampe Jr, R.T. / Griffin, R.J. / Harris, P.A. / ...Authors: Davis, S.T. / Benson, B.G. / Bramson, H.N. / Chapman, D.E. / Dickerson, S.H. / Dold, K.M. / Eberwein, D.J. / Edelstein, M. / Frye, S.V. / Gampe Jr, R.T. / Griffin, R.J. / Harris, P.A. / Hassell, A.M. / Holmes, W.D. / Hunter, R.N. / Knick, V.B. / Lackey, K. / Lovejoy, B. / Luzzio, M.J. / Murray, D. / Parker, P. / Rocque, W.J. / Shewchuk, L. / Veal, J.M. / Walker, D.H. / Kuyper, L.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fvt.cif.gz | 70.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fvt.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 1fvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fvt_validation.pdf.gz | 722.8 KB | Display | wwPDB validaton report |
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Full document | 1fvt_full_validation.pdf.gz | 731.2 KB | Display | |
Data in XML | 1fvt_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 1fvt_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/1fvt ftp://data.pdbj.org/pub/pdb/validation_reports/fv/1fvt | HTTPS FTP |
-Related 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: 33976.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid details: BACILOVIRUS / Plasmid: PFASTBAC1 OR PACHLT-A / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-106 / |
#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: 2.11 Å3/Da / Density % sol: 41.74 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG 3340, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Details: Shewchuk L., (2000) J. Med. Chem., 43, 133. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 11, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→28 Å / Num. all: 13325 / Num. obs: 13325 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 41.2 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.217 / Num. unique all: 2013 / % possible all: 87 |
Reflection | *PLUS Num. measured all: 157652 |
-Processing
Software |
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Refinement | Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 9.1 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.4 |