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Yorodumi- PDB-1di8: THE STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2) IN COMPLEX WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1di8 | ||||||
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Title | THE STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2) IN COMPLEX WITH 4-[3-HYDROXYANILINO]-6,7-DIMETHOXYQUINAZOLINE | ||||||
Components | CYCLIN-DEPENDENT KINASE 2 | ||||||
Keywords | TRANSFERASE / SERINE/THREONINE PROTEIN KINASE / CELL CYCLE / ATP-BINDING | ||||||
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 | Shewchuk, L. / Hassell, A. / Kuyper, L.F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2000 Title: Binding mode of the 4-anilinoquinazoline class of protein kinase inhibitor: X-ray crystallographic studies of 4-anilinoquinazolines bound to cyclin-dependent kinase 2 and p38 kinase. Authors: Shewchuk, L. / Hassell, A. / Wisely, B. / Rocque, W. / Holmes, W. / Veal, J. / 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 | 1di8.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1di8.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 1di8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1di8_validation.pdf.gz | 685.8 KB | Display | wwPDB validaton report |
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Full document | 1di8_full_validation.pdf.gz | 694.3 KB | Display | |
Data in XML | 1di8_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 1di8_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/1di8 ftp://data.pdbj.org/pub/pdb/validation_reports/di/1di8 | 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) / Cell (production host): T.NI / Production host: unidentified baculovirus References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Chemical | ChemComp-DTQ / |
#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: 2.14 Å3/Da / Density % sol: 42.53 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20MM HEPES, 1MM EDTA, 10% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 16, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 17097 / Num. obs: 14980 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 36 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 10 % / Rmerge(I) obs: 0.2 / % possible all: 96.3 |
Reflection | *PLUS Num. measured all: 160386 / Rmerge(I) obs: 0.093 |
-Processing
Software |
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Refinement | Resolution: 2.2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 0 / Rfactor obs: 0.185 / Rfactor Rfree: 0.227 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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