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Yorodumi- PDB-3hp1: Crystal structure of human dCK R104M/D133A in complex with L-dT a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hp1 | |||||||||
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Title | Crystal structure of human dCK R104M/D133A in complex with L-dT and ADP | |||||||||
Components | Deoxycytidine kinase | |||||||||
Keywords | TRANSFERASE / dCK / L-dT / DM-dCK / dCK Structure Function Studies / Nucleoside Kinase / Protein-NA complex / dCK drug designing / ATP-binding / Kinase / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | |||||||||
Authors | Hazra, S. / Lavie, A. | |||||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Extending Thymidine Kinase Activity to the Catalytic Repertoire of Human Deoxycytidine Kinase. Authors: Hazra, S. / Sabini, E. / Ort, 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 | 3hp1.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hp1.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 3hp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/3hp1 ftp://data.pdbj.org/pub/pdb/validation_reports/hp/3hp1 | HTTPS FTP |
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-Related structure data
Related structure data | 1p5zS 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: 32637.775 Da / Num. of mol.: 1 / Mutation: R104M, D133A 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 |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-LLT / |
#4: 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: 2.28 Å3/Da / Density % sol: 46.15 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1 microliter of protein-nucleoside-nucleotide mix and 1 microliter reservoir solution containing 0.9-1.5 M Trisodium citrate dihydrate and 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-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: Aug 28, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 13710 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.42 |
Reflection shell | Resolution: 2.3→2.45 Å / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 6.93 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1P5Z Resolution: 2.31→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.55 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.259 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.265 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31→2.37 Å / Total num. of bins used: 20
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