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- PDB-1kqn: Crystal structure of NMN/NaMN adenylyltransferase complexed with NAD -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kqn | ||||||
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Title | Crystal structure of NMN/NaMN adenylyltransferase complexed with NAD | ||||||
![]() | NICOTINAMIDE MONONUCLEOTIDE ADENYLYL TRANSFERASE | ||||||
![]() | TRANSFERASE / nucleotidyltransferase superfamily | ||||||
Function / homology | ![]() negative regulation of apoptotic DNA fragmentation / protein ADP-ribosyltransferase-substrate adaptor activity / nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nucleotide biosynthetic process / nicotinate-nucleotide adenylyltransferase activity / Nicotinate metabolism / ATP generation from poly-ADP-D-ribose / NAD biosynthetic process ...negative regulation of apoptotic DNA fragmentation / protein ADP-ribosyltransferase-substrate adaptor activity / nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nucleotide biosynthetic process / nicotinate-nucleotide adenylyltransferase activity / Nicotinate metabolism / ATP generation from poly-ADP-D-ribose / NAD biosynthetic process / response to wounding / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / nuclear body / negative regulation of DNA-templated transcription / chromatin / nucleoplasm / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, T. / Kurnasov, O. / Tomchick, D.R. / Binns, D.D. / Grishin, N.V. / Marquez, V.E. / Osterman, A.L. / Zhang, H. | ||||||
![]() | ![]() Title: Structure of Human Nicotinamide/Nicotonic Acid Mononucleotide Adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin. Authors: Zhou, T. / Kurnasov, O. / Tomchick, D.R. / Binns, D.D. / Grishin, N.V. / Marquez, V.E. / Osterman, A.L. / Zhang, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301.4 KB | Display | ![]() |
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PDB format | ![]() | 245.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 64.2 KB | Display | |
Data in CIF | ![]() | 86.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 | The biological assembly is hexamer, containing chains A, B, C, D, E, F, in the asymmetric unit. |
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Components
#1: Protein | Mass: 31982.502 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9HAN9, nicotinamide-nucleotide adenylyltransferase #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-XE / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Na Formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 132989 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.28 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 1.9 / % possible all: 84.8 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. measured all: 435916 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 84.8 % / Mean I/σ(I) obs: 1.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.25 / Highest resolution: 2.2 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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