[English] 日本語
Yorodumi- PDB-4jlk: Human dCK C4S-S74E mutant in complex with UDP and the F2.2.1 inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jlk | ||||||
---|---|---|---|---|---|---|---|
Title | Human dCK C4S-S74E mutant in complex with UDP and the F2.2.1 inhibitoR (2-[({2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-5-METHYL-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE) | ||||||
Components | Deoxycytidine kinase | ||||||
Keywords | transferase/transferase inhibitor / phosphoryl transfer / phosphorylation / kinase / transferase-transferase inhibitor complex | ||||||
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: 1.89 Å | ||||||
Authors | Nomme, J. / Lavie, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Development of new deoxycytidine kinase inhibitors and noninvasive in vivo evaluation using positron emission tomography. Authors: Murphy, J.M. / Armijo, A.L. / Nomme, J. / Lee, C.H. / Smith, Q.A. / Li, Z. / Campbell, D.O. / Liao, H.I. / Nathanson, D.A. / Austin, W.R. / Lee, J.T. / Darvish, R. / Wei, L. / Wang, J. / Su, ...Authors: Murphy, J.M. / Armijo, A.L. / Nomme, J. / Lee, C.H. / Smith, Q.A. / Li, Z. / Campbell, D.O. / Liao, H.I. / Nathanson, D.A. / Austin, W.R. / Lee, J.T. / Darvish, R. / Wei, L. / Wang, J. / Su, Y. / Damoiseaux, R. / Sadeghi, S. / Phelps, M.E. / Herschman, H.R. / Czernin, J. / Alexandrova, A.N. / Jung, M.E. / Lavie, A. / Radu, C.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4jlk.cif.gz | 118.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4jlk.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jlk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/4jlk ftp://data.pdbj.org/pub/pdb/validation_reports/jl/4jlk | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32701.627 Da / Num. of mol.: 2 / Mutation: C9S, C45S, C59S, S74E, 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 C41 / References: UniProt: P27707, deoxycytidine kinase #2: Chemical | #3: Chemical | ChemComp-1NO / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.35 % |
---|---|
Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.9-1.5 M trisodium citrate dehydrate, 25 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 2, 2011 | |||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 1.89→30 Å / Num. all: 44054 / Num. obs: 44054 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | |||||||||||||||
Reflection shell | Resolution: 1.89→2.01 Å / % possible all: 96.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→29.73 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.836 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.03 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| |||||||||||||||||||||||||||||||||||||||||||||
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: 34.643 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→29.73 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.893→1.942 Å / Total num. of bins used: 20
|