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Yorodumi- PDB-1gii: HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE CDK4 INHIBITOR -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gii | ||||||
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Title | HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE CDK4 INHIBITOR | ||||||
Components | CELL DIVISION PROTEIN KINASE 2 | ||||||
Keywords | TRANSFERASE / protein kinase / cell cycle / 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 / Resolution: 2 Å | ||||||
Authors | Ikuta, M. / Nishimura, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Crystallographic approach to identification of cyclin-dependent kinase 4 (CDK4)-specific inhibitors by using CDK4 mimic CDK2 protein. Authors: Ikuta, M. / Kamata, K. / Fukasawa, K. / Honma, T. / Machida, T. / Hirai, H. / Suzuki-Takahashi, I. / Hayama, T. / Nishimura, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gii.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gii.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gii_validation.pdf.gz | 461 KB | Display | wwPDB validaton report |
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Full document | 1gii_full_validation.pdf.gz | 467.9 KB | Display | |
Data in XML | 1gii_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1gii_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/1gii ftp://data.pdbj.org/pub/pdb/validation_reports/gi/1gii | 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: 33925.359 Da / Num. of mol.: 1 / Mutation: F82H, L83V, K89T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24941, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-1PU / |
#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: 2.13 Å3/Da / Density % sol: 42.19 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: HEPES, sodium chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 278K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 |
Detector | Detector: IMAGE PLATE / Date: Jul 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→100 Å / Num. all: 68987 / Num. obs: 19273 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 23.602 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.157 / Num. unique all: 660 / % possible all: 82.4 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 68987 |
-Processing
Software |
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Refinement | Resolution: 2→8 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints | Type: x_bond_d / Dev ideal: 0.015 | ||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 98 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.202 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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