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- PDB-6pwz: Crystal structure of human uridine-cytidine kinase 2 complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pwz | ||||||
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Title | Crystal structure of human uridine-cytidine kinase 2 complexed with 2'-azidocytidine | ||||||
![]() | Uridine-cytidine kinase 2 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / uridine cytidine kinase / nucleotide binding / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() uridine/cytidine kinase / CTP salvage / ribosylnicotinamide kinase activity / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / phosphorylation / ATP binding / identical protein binding ...uridine/cytidine kinase / CTP salvage / ribosylnicotinamide kinase activity / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / phosphorylation / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cuthbert, B.J. / Goulding, C.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Incorporation of novel azido-nucleotides into RNA Authors: Nainar, S. / Cuthbert, B.J. / Goulding, C.W. / Spitale, R.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 429 KB | Display | ![]() |
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PDB format | ![]() | 283.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 66.6 KB | Display | |
Data in CIF | ![]() | 88.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n55S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28108.830 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris, pH 6.5, 25% pentaerythritol ethoxylate (15/4 EO/OH) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2018 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→83.2 Å / Num. obs: 48286 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 69.63 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.057 / Rrim(I) all: 0.081 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 4783 / CC1/2: 0.619 / Rpim(I) all: 0.432 / Rrim(I) all: 0.611 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 6N55 Resolution: 3→83.2 Å / SU ML: 0.3918 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.985
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→83.2 Å
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Refine LS restraints |
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LS refinement shell |
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