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Yorodumi- PDB-4kcg: Human dCK C4S-S74E mutant in complex with UDP and the DI-39 inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kcg | ||||||
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Title | Human dCK C4S-S74E mutant in complex with UDP and the DI-39 inhibitor | ||||||
Components | Deoxycytidine kinase | ||||||
Keywords | transferase/transferase inhibitor / phosphoryl transfer / phosphorylation / deoxycytidine / 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: 2.09 Å | ||||||
Authors | Nomme, J. / Lavie, A. | ||||||
Citation | Journal: J.Exp.Med. / Year: 2014 Title: Co-targeting of convergent nucleotide biosynthetic pathways for leukemia eradication. Authors: Nathanson, D.A. / Armijo, A.L. / Tom, M. / Li, Z. / Dimitrova, E. / Austin, W.R. / Nomme, J. / Campbell, D.O. / Ta, L. / Le, T.M. / Lee, J.T. / Darvish, R. / Gordin, A. / Wei, L. / Liao, H.I. ...Authors: Nathanson, D.A. / Armijo, A.L. / Tom, M. / Li, Z. / Dimitrova, E. / Austin, W.R. / Nomme, J. / Campbell, D.O. / Ta, L. / Le, T.M. / Lee, J.T. / Darvish, R. / Gordin, A. / Wei, L. / Liao, H.I. / Wilks, M. / Martin, C. / Sadeghi, S. / Murphy, J.M. / Boulos, N. / Phelps, M.E. / Faull, K.F. / Herschman, H.R. / Jung, M.E. / Czernin, J. / Lavie, A. / Radu, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kcg.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kcg.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 4kcg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/4kcg ftp://data.pdbj.org/pub/pdb/validation_reports/kc/4kcg | HTTPS FTP |
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-Related structure data
Related structure data | 4jljS S: Starting model for refinement |
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Similar structure data |
-Links
-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.: 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 | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.51 % |
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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 | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å | |||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2012 | |||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.09→30 Å / Num. all: 32222 / Num. obs: 32222 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.045 / Net I/σ(I): 18.73 | |||||||||||||||
Reflection shell | Resolution: 2.09→2.22 Å / Mean I/σ(I) obs: 2.24 / Rsym value: 0.689 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4jlj Resolution: 2.09→27.61 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.313 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.043 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 54.048 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→27.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.092→2.147 Å / Total num. of bins used: 20
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