+
Open data
-
Basic information
Entry | Database: PDB / ID: 2zi6 | ||||||
---|---|---|---|---|---|---|---|
Title | C4S dCK variant of dCK in complex with D-dA+UDP | ||||||
![]() | Deoxycytidine kinase | ||||||
![]() | TRANSFERASE / dCK / purine / deoxyadenosine / deoxycytidine kinase / nucleoside / enantiomer / D-dA / UDP / ATP-binding / Nucleotide-binding / Nucleus / Phosphoprotein | ||||||
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 / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sabini, E. / Lavie, A. | ||||||
![]() | ![]() Title: Structural basis for substrate promiscuity of dCK Authors: Sabini, E. / Hazra, S. / Ort, S. / Konrad, M. / Lavie, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 204.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 159.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2zi3C ![]() 2zi4C ![]() 2zi5C ![]() 1p5zS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 32572.510 Da / Num. of mol.: 4 / Mutation: C9S, C45S, C59S, C146S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-UDP / #3: Chemical | ChemComp-3D1 / ( #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.58 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→30 Å / Num. all: 109802 / Num. obs: 109802 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.77→1.87 Å / Redundancy: 4 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3 / Num. unique all: 16552 / % possible all: 93 |
-
Processing
Software |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENRTY 1P5Z Resolution: 1.77→30 Å / σ(F): 0 / σ(I): 0
| |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→30 Å
| |||||||||||||||
Refine LS restraints |
|