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Yorodumi- PDB-8dsc: Human NAMPT in complex with substrate NAM and small molecule acti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dsc | ||||||
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Title | Human NAMPT in complex with substrate NAM and small molecule activator NP-A1-R | ||||||
Components | Nicotinamide phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / NAD biosynthesis enzyme:activator complex | ||||||
Function / homology | Function and homology information nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / positive regulation of nitric-oxide synthase biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression ...nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NAD biosynthetic process / positive regulation of nitric-oxide synthase biosynthetic process / NPAS4 regulates expression of target genes / BMAL1:CLOCK,NPAS2 activates circadian gene expression / cytokine activity / circadian regulation of gene expression / cell junction / cell-cell signaling / nuclear speck / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.321 Å | ||||||
Authors | Ratia, K. / Xiong, R. / Shen, Z. / Thatcher, G.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2023 Title: Mechanism of Allosteric Modulation of Nicotinamide Phosphoribosyltransferase to Elevate Cellular NAD. Authors: Ratia, K.M. / Shen, Z. / Gordon-Blake, J. / Lee, H. / Laham, M.S. / Krider, I.S. / Christie, N. / Ackerman-Berrier, M. / Penton, C. / Knowles, N.G. / Musku, S.R. / Fu, J. / Velma, G.R. / ...Authors: Ratia, K.M. / Shen, Z. / Gordon-Blake, J. / Lee, H. / Laham, M.S. / Krider, I.S. / Christie, N. / Ackerman-Berrier, M. / Penton, C. / Knowles, N.G. / Musku, S.R. / Fu, J. / Velma, G.R. / Xiong, R. / Thatcher, G.R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dsc.cif.gz | 227.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dsc.ent.gz | 176.8 KB | Display | PDB format |
PDBx/mmJSON format | 8dsc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dsc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8dsc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8dsc_validation.xml.gz | 45.2 KB | Display | |
Data in CIF | 8dsc_validation.cif.gz | 69.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/8dsc ftp://data.pdbj.org/pub/pdb/validation_reports/ds/8dsc | HTTPS FTP |
-Related structure data
Related structure data | 8dsdC 8dseC 8dshC 8dsiC 8dtjC 2e5dS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 56666.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAMPT, PBEF, PBEF1 / Production host: Escherichia coli (E. coli) References: UniProt: P43490, nicotinamide phosphoribosyltransferase |
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-Non-polymers , 7 types, 1051 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.33 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl, pH 8.5, 0.2 M NaCl, 20% glycerol and 13-18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 17, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.32→51.3 Å / Num. obs: 245312 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.039 / Rrim(I) all: 0.076 / Net I/σ(I): 9.6 / Num. measured all: 918063 / Scaling rejects: 362 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E5D Resolution: 1.321→36.917 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.65 Å2 / Biso mean: 15.8627 Å2 / Biso min: 6.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.321→36.917 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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