+Open data
-Basic information
Entry | Database: PDB / ID: 3nfr | ||||||
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Title | Casimiroin analog inhibitor of quinone reductase 2 | ||||||
Components | Ribosyldihydronicotinamide dehydrogenase [quinone] | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / NQ02 / quinone reductase 2 / QR2 / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding ...ribosyldihydronicotinamide dehydrogenase (quinone) / dihydronicotinamide riboside quinone reductase activity / quinone catabolic process / resveratrol binding / oxidoreductase activity, acting on other nitrogenous compounds as donors / melatonin binding / NAD(P)H dehydrogenase (quinone) activity / Phase I - Functionalization of compounds / chloride ion binding / FAD binding / electron transfer activity / oxidoreductase activity / protein homodimerization activity / extracellular exosome / zinc ion binding / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Sturdy, M. / Mesecar, A.D. / Jermihov, K. / Cushman, M. / Maiti, A. | ||||||
Citation | Journal: To be Published Title: X-ray Crystallographic Structure Activity Relationship (SAR) of Casimiroin and its Analogs Bound to Human Quinone Reductase 2 Authors: Sturdy, M. / Maiti, A. / Jermihov, K. / Cushman, M. / Mesecar, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nfr.cif.gz | 114.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nfr.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 3nfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/3nfr ftp://data.pdbj.org/pub/pdb/validation_reports/nf/3nfr | HTTPS FTP |
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-Related structure data
Related structure data | 3nhfC 3nhjC 3nhkC 3nhlC 3nhpC 3nhrC 3nhsC 3nhuC 3nhwC 3nhyC 3o2nC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25849.338 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Plasmid: pET-23d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16083, EC: 1.10.99.2 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.4 Å3/Da / Density % sol: 48.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 1.339 M ammonium sulfate, 0.1 M Bis-Tris, 0.1 M NaCl, 5 mM DTT, 12 M FAD, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→65.56 Å / Num. obs: 63822 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.57→1.6 Å / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→65.56 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.643 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 24.045 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→65.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.57→1.61 Å / Total num. of bins used: 20
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