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- PDB-2qsz: Human nicotinamide riboside kinase 1 in complex with nicotinamide... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qsz | ||||||
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Title | Human nicotinamide riboside kinase 1 in complex with nicotinamide mononucleotide | ||||||
![]() | Nicotinamide riboside kinase 1 | ||||||
![]() | TRANSFERASE / non-protein kinase / NAD+ / nicotinamide riboside / nrk1 / nicotinamide riboside kinase activity / nicotinic acid riboside kinase activity / NAD biosynthesis / ADP / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Alternative splicing / ATP-binding / Nucleotide-binding / Pyridine nucleotide biosynthesis | ||||||
Function / homology | ![]() nicotinate riboside kinase / ribosylnicotinate kinase activity / ribosylnicotinamide kinase / ribosylnicotinamide kinase activity / Nicotinate metabolism / NAD metabolic process / NAD biosynthetic process / phosphorylation / ATP binding / metal ion binding ...nicotinate riboside kinase / ribosylnicotinate kinase activity / ribosylnicotinamide kinase / ribosylnicotinamide kinase activity / Nicotinate metabolism / NAD metabolic process / NAD biosynthetic process / phosphorylation / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rabeh, W.M. / Tempel, W. / Nedyalkova, L. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Brenner, C. ...Rabeh, W.M. / Tempel, W. / Nedyalkova, L. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Brenner, C. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Nicotinamide Riboside Kinase Structures Reveal New Pathways to NAD(+). Authors: Tempel, W. / Rabeh, W.M. / Bogan, K.L. / Belenky, P. / Wojcik, M. / Seidle, H.F. / Nedyalkova, L. / Yang, T. / Sauve, A.A. / Park, H.W. / Brenner, C. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.6 KB | Display | ![]() |
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PDB format | ![]() | 41 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 802.8 KB | Display | ![]() |
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Full document | ![]() | 802.9 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2p0eC ![]() 2qsySC ![]() 2qt0C ![]() 2qt1C S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Details | not known |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24373.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NWW6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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-Non-polymers , 5 types, 113 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NMN.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NMN.gif)
![](data/chem/img/UNX.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PO4 / | ||
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#3: Chemical | ChemComp-CL / | ||
#4: Chemical | ChemComp-NMN / | ||
#5: Chemical | ChemComp-UNX / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 3350, 0.2M Sodium phosphate monobasic, 0.15M D(+)sucrose, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 26, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→30 Å / Num. obs: 19738 / % possible obs: 99.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.138 / Χ2: 1.911 / Net I/σ(I): 6.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2QSY Resolution: 1.9→23.64 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.218 / WRfactor Rwork: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Prodrg, arp/warp, coot, molprobity programs have also been used in refinement
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.061 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→23.64 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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