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Yorodumi- PDB-2a7q: Crystal structure of human dCK complexed with clofarabine and ADP -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a7q | ||||||
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Title | Crystal structure of human dCK complexed with clofarabine and ADP | ||||||
Components | Deoxycytidine kinase | ||||||
Keywords | TRANSFERASE / alpha/beta parallel beta-sheet of 5 strands | ||||||
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: 2.55 Å | ||||||
Authors | Zhang, Y. / Secrist III, J.A. / Ealick, S.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: The structure of human deoxycytidine kinase in complex with clofarabine reveals key interactions for prodrug activation. Authors: Zhang, Y. / Secrist, J.A. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a7q.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a7q.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 2a7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/2a7q ftp://data.pdbj.org/pub/pdb/validation_reports/a7/2a7q | HTTPS FTP |
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-Related structure data
Related structure data | 1p61S 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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Details | The biological assembly is a dimer with the second monomer generated by the operation: -y, -x, -z+1/2 |
-Components
#1: Protein | Mass: 30834.779 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27707, deoxycytidine kinase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-CFB / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium citrate, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2005 / Details: Mirrors |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→500 Å / Num. all: 9726 / Num. obs: 9726 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 29.2 Å2 / Rsym value: 0.049 / Net I/σ(I): 35.2 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 6.4 / Num. unique all: 557 / Rsym value: 0.161 / % possible all: 54.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1P61 Resolution: 2.55→48.49 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 462177.47 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.4184 Å2 / ksol: 0.361286 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→48.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
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Xplor file |
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