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- PDB-7zi6: Crystal structure of dCK C4S-S74E mutant in complex with UDP and ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zi6 | ||||||
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Title | Crystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0325 inhibitor | ||||||
![]() | Deoxycytidine kinase | ||||||
![]() | TRANSFERASE / Inhibitor | ||||||
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 / phosphorylation / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Saez-Ayala, M. / Ben-Yaala, K. / Betzi, S. / Rebuffet, E. / Morelli, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: From a drug repositioning to a structure-based drug design approach to tackle acute lymphoblastic leukemia. Authors: Saez-Ayala, M. / Hoffer, L. / Abel, S. / Ben Yaala, K. / Sicard, B. / Andrieu, G.P. / Latiri, M. / Davison, E.K. / Ciufolini, M.A. / Bremond, P. / Rebuffet, E. / Roche, P. / Derviaux, C. / ...Authors: Saez-Ayala, M. / Hoffer, L. / Abel, S. / Ben Yaala, K. / Sicard, B. / Andrieu, G.P. / Latiri, M. / Davison, E.K. / Ciufolini, M.A. / Bremond, P. / Rebuffet, E. / Roche, P. / Derviaux, C. / Voisset, E. / Montersino, C. / Castellano, R. / Collette, Y. / Asnafi, V. / Betzi, S. / Dubreuil, P. / Combes, S. / Morelli, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.4 KB | Display | ![]() |
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PDB format | ![]() | 47.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 792.4 KB | Display | ![]() |
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Full document | ![]() | 792.2 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zi1C ![]() 7zi2C ![]() 7zi3C ![]() 7zi5C ![]() 7zi7C ![]() 7zi8C ![]() 7zi9C ![]() 7ziaC ![]() 7zibC ![]() 4kcgS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32701.627 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P27707, deoxycytidine kinase, 2'-deoxyadenosine kinase, deoxyguanosine kinase |
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#2: Chemical | ChemComp-UDP / |
#3: Chemical | ChemComp-JAQ / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.33 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.1 M Sodium citrate, 73 mM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 3, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.975631 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→48.53 Å / Num. obs: 17508 / % possible obs: 98 % / Redundancy: 25.797 % / Biso Wilson estimate: 57.632 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.11 / Χ2: 0.81 / Net I/σ(I): 19.65 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4KCG Resolution: 2.1→48.53 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.959 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 132.41 Å2 / Biso mean: 55.748 Å2 / Biso min: 37.35 Å2
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Refinement step | Cycle: final / Resolution: 2.1→48.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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