[English] 日本語
Yorodumi- PDB-8ooj: Crystal structure of dCK C4S-S74E mutant in complex with EdC and UDP -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ooj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of dCK C4S-S74E mutant in complex with EdC and UDP | ||||||
Components | Deoxycytidine kinase | ||||||
Keywords | TRANSFERASE / Nucleoside kinase / phosphorylation / 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: 2.1 Å | ||||||
Authors | Saez-Ayala, M. / Rebuffet, E. / Betzi, S. / Morelli, X. | ||||||
Funding support | France, 1items
| ||||||
Citation | Journal: Mol.Cancer Ther. / Year: 2024 Title: 4'-Ethynyl-2'-Deoxycytidine (EdC) Preferentially Targets Lymphoma and Leukemia Subtypes by Inducing Replicative Stress. Authors: Calbert, M.L. / Chandramouly, G. / Adams, C.M. / Saez-Ayala, M. / Kent, T. / Tyagi, M. / Ayyadevara, V.S.S.A. / Wang, Y. / Krais, J.J. / Gordon, J. / Atkins, J. / Toma, M.M. / Betzi, S. / ...Authors: Calbert, M.L. / Chandramouly, G. / Adams, C.M. / Saez-Ayala, M. / Kent, T. / Tyagi, M. / Ayyadevara, V.S.S.A. / Wang, Y. / Krais, J.J. / Gordon, J. / Atkins, J. / Toma, M.M. / Betzi, S. / Boghossian, A.S. / Rees, M.G. / Ronan, M.M. / Roth, J.A. / Goldman, A.R. / Gorman, N. / Mitra, R. / Childers, W.E. / Grana, X. / Skorski, T. / Johnson, N. / Hurtz, C. / Morelli, X. / Eischen, C.M. / Pomerantz, R.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ooj.cif.gz | 209.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ooj.ent.gz | 166.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ooj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/8ooj ftp://data.pdbj.org/pub/pdb/validation_reports/oo/8ooj | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32701.627 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Production host: Bacteria (eubacteria) / Strain (production host): BL21 References: UniProt: P27707, deoxycytidine kinase, 2'-deoxyadenosine kinase, deoxyguanosine kinase #2: Chemical | ChemComp-UDP / #3: Chemical | ChemComp-VVC / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.15 % |
---|---|
Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES 70 mM pH 7.5 Sodium citrate 1.1 M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.76 Å / Num. obs: 65390 / % possible obs: 99.8 % / Redundancy: 14.99 % / CC1/2: 0.999 / Net I/σ(I): 9.64 |
Reflection shell | Resolution: 2.1→2.22 Å / Num. unique obs: 10404 / CC1/2: 0.683 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.76 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.587 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.215 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.444 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→48.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|