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- PDB-2noa: The structure of deoxycytidine kinase complexed with lamivudine a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2noa | ||||||
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Title | The structure of deoxycytidine kinase complexed with lamivudine and ADP. | ||||||
![]() | deoxycytidine kinase | ||||||
![]() | TRANSFERASE / dCK / 3TC / human deoxycytidine kinase / L-dC / enantiomer / antiviral / Lamivudine / Epivir | ||||||
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. / Lavie, A. | ||||||
![]() | ![]() Title: Structural basis for activation of the therapeutic L-nucleoside analogs 3TC and troxacitabine by human deoxycytidine kinase. Authors: Sabini, E. / Hazra, S. / Konrad, M. / Burley, S.K. / 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 | ![]() | 116.9 KB | Display | ![]() |
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PDB format | ![]() | 89.3 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 | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2no9C ![]() 1p5zS S: Starting model for refinement C: citing same article ( |
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Similar 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 on special symmetry positions |
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Components
#1: Protein | Mass: 32659.588 Da / Num. of mol.: 2 / Mutation: C9S,C45S,C59S,C146S 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: 45.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Reservoir containing 0.95-1.5M trisodium citrate dihydrate and 100mM HEPES, pH 7.5., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2005 / Details: mirrors |
Radiation | Monochromator: Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing, Rosenbaum-Rock vertical focusing mirror. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 52519 / Num. obs: 50033 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.059 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 6265 / Rsym value: 0.435 / % possible all: 74.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1P5Z Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.161 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.138 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.832 Å / Total num. of bins used: 20
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