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- PDB-1p60: Structure of human dCK complexed with 2'-Deoxycytidine and ADP, S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p60 | ||||||
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Title | Structure of human dCK complexed with 2'-Deoxycytidine and ADP, Space group C 2 2 21 | ||||||
![]() | Deoxycytidine kinase | ||||||
![]() | TRANSFERASE / nucleoside kinase / P-loop / deoxycytidine | ||||||
Function / homology | ![]() deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity ...deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity / pyrimidine nucleotide metabolic process / Purine salvage / phosphorylation / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sabini, E. / Ort, S. / Monnerjahn, C. / Konrad, M. / Lavie, A. | ||||||
![]() | ![]() Title: Structure of human dCK suggests strategies to improve anticancer and antiviral therapy Authors: Sabini, E. / Ort, S. / Monnerjahn, C. / Konrad, M. / Lavie, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.6 KB | Display | ![]() |
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PDB format | ![]() | 91.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 34.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30834.779 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.97 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.95-1.0M citrate trisodium dihydrate, 100mM Hepes, 5mM deoxycytidine, 5mM ADP, 5mM MgCl2,5mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 16, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→30 Å / Num. obs: 39365 / Redundancy: 6.9 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.045 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.96→2 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.291 |
Reflection | *PLUS Num. obs: 39237 / % possible obs: 97.4 % / Num. measured all: 270973 / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS Lowest resolution: 2 Å / % possible obs: 67.8 % / Rmerge(I) obs: 0.291 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.099 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.965→2.016 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.203 / Rfactor Rwork: 0.161 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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