+Open data
-Basic information
Entry | Database: PDB / ID: 2zia | ||||||
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Title | C4S dCK variant of dCK in complex with cladribine+UDP | ||||||
Components | Deoxycytidine kinase | ||||||
Keywords | TRANSFERASE / dCK / purine / deoxycytidine kinase / nucleoside / cladribine / 2-chloro-2'-deoxyadenosine / deoxyadenosine analog / UDP / ATP-binding / Nucleotide-binding / Nucleus / Phosphoprotein | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sabini, E. / Lavie, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Elucidation of different binding modes of purine nucleosides to human deoxycytidine kinase Authors: Sabini, E. / Hazra, S. / Konrad, M. / Lavie, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zia.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zia.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 2zia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zia_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2zia_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2zia_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 2zia_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/2zia ftp://data.pdbj.org/pub/pdb/validation_reports/zi/2zia | HTTPS FTP |
-Related structure data
Related structure data | 2zi7C 2zi9C 1p5zS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 32572.510 Da / Num. of mol.: 2 / Mutation: C9S, C45S, C59S, C146S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27707, deoxycytidine kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.04 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.0M Sodium Citrate, 100mM Hepes, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→30 Å / Num. all: 52169 / Num. obs: 52169 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.79→1.9 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 3.3 / Num. unique all: 8138 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P5Z Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.183 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.137 / ESU R Free: 0.137 / 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: 23.586 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: 1.797→1.844 Å / Total num. of bins used: 20
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