[English] 日本語
Yorodumi- PDB-2vpp: Drosophila melanogaster deoxyribonucleoside kinase successfully a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vpp | ||||||
---|---|---|---|---|---|---|---|
Title | Drosophila melanogaster deoxyribonucleoside kinase successfully activates gemcitabine in transduced cancer cell lines | ||||||
Components | DEOXYNUCLEOSIDE KINASE | ||||||
Keywords | TRANSFERASE / KINASE / CANCER / ATP-BINDING / PHOSPHOPROTEIN / NUCLEOSIDE ANALOGS / NUCLEOTIDE-BINDING / STRUCTURE-FUNCTION RELATIONSHIP / GEMCITABINE / GENE THERAPY / DNA SYNTHESIS | ||||||
Function / homology | Function and homology information deoxynucleoside kinase / Pyrimidine salvage / deoxynucleoside kinase activity / nucleoside salvage / uridine kinase activity / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / thymidine kinase activity / deoxyguanosine kinase activity / deoxyadenosine kinase activity ...deoxynucleoside kinase / Pyrimidine salvage / deoxynucleoside kinase activity / nucleoside salvage / uridine kinase activity / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / thymidine kinase activity / deoxyguanosine kinase activity / deoxyadenosine kinase activity / cytidine kinase activity / DNA biosynthetic process / kinase activity / phosphorylation / mitochondrion / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Knecht, W. / Mikkelsen, N.E. / Clausen, A. / Willer, M. / Gojkovic, Z. / Piskur, J. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2009 Title: Drosophila Melanogaster Deoxyribonucleoside Kinase Activates Gemcitabine. Authors: Knecht, W. / Mikkelsen, N.E. / Clausen, A. / Willer, M. / Eklund, H. / Gojkovic, Z. / Piskur, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vpp.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vpp.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/2vpp ftp://data.pdbj.org/pub/pdb/validation_reports/vp/2vpp | HTTPS FTP |
---|
-Related structure data
Related structure data | 1j90S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.997, 0.004062, -0.07696), Vector: |
-Components
#1: Protein | Mass: 26906.707 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-230 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9XZT6, deoxynucleoside kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 48 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 8, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→2.26 Å / Num. obs: 24968 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J90 Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.005 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 28.25 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|