+Open data
-Basic information
Entry | Database: PDB / ID: 2gvg | ||||||
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Title | Crystal Structure of human NMPRTase and its complex with NMN | ||||||
Components | Nicotinamide phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / NMPRTase / Visfatin / PBEF / CRYSTAL / Cancer | ||||||
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: 2.2 Å | ||||||
Authors | Khan, J.A. / Tao, X. / Tong, L. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Molecular basis for the inhibition of human NMPRTase, a novel target for anticancer agents. Authors: Khan, J.A. / Tao, X. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gvg.cif.gz | 574.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gvg.ent.gz | 475 KB | Display | PDB format |
PDBx/mmJSON format | 2gvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gvg_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 2gvg_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 2gvg_validation.xml.gz | 121.3 KB | Display | |
Data in CIF | 2gvg_validation.cif.gz | 165.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/2gvg ftp://data.pdbj.org/pub/pdb/validation_reports/gv/2gvg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 55594.938 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAMPT / Production host: Escherichia coli (E. coli) References: UniProt: P43490, nicotinamide phosphoribosyltransferase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-NMN / #4: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 46.97 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.2 Details: 50mM phosphate buffer ph 9.2 24% PEG 3350, 200mM NaCl BaCl2 as additive, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 12, 2005 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 142302 / Num. obs: 142302 / % possible obs: 93 % / Observed criterion σ(I): 0.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / σ(F): 0.5 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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