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- PDB-2vp2: Structural Studies of Nucleoside Analog and Feedback Inhibitor Bi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vp2 | ||||||
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Title | Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase | ||||||
![]() | DEOXYNUCLEOSIDE KINASE | ||||||
![]() | TRANSFERASE / ATP-BINDING / DNA SYNTHESIS / PHOSPHOPROTEIN / FEEDBACK INHIBITION / DEOXYRIBONUCLEOSIDE KINASE / SALVAGE PATHWAY / NUCLEOTIDE-BINDING / DTTP / KINASE / COMPLEX / DROSOPHILA | ||||||
Function / homology | ![]() 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 / mitochondrion / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mikkelsen, N.E. / Munch-Petersen, B. / Eklund, H. | ||||||
![]() | ![]() Title: Structural Studies of Nucleoside Analog and Feedback Inhibitor Binding to Drosophila Melanogaster Multisubstrate Deoxyribonucleoside Kinase. Authors: Mikkelsen, N.E. / Munch-Petersen, B. / Eklund, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.1 KB | Display | ![]() |
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PDB format | ![]() | 73.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2jj8C ![]() 2vp0C ![]() 2vp4C ![]() 2vp5C ![]() 2vp6C ![]() 2vp9C ![]() 2vqsC ![]() 1j90S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9901, 0.005906, -0.14), Vector: |
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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.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.47 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 4, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.981661 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 18113 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1J90 Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.874 / SU B: 8.964 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.48 / ESU R Free: 0.299 / 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: 34.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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