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Yorodumi- PDB-5lbu: Structure of the human quinone reductase 2 (NQO2) in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lbu | ||||||||||||
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Title | Structure of the human quinone reductase 2 (NQO2) in complex with to CL097 | ||||||||||||
Components | Ribosyldihydronicotinamide dehydrogenase [quinone] | ||||||||||||
Keywords | OXIDOREDUCTASE / quinone reductase 2 ribosyldihydronicotinamide dehydrogenase / oxydoreductase | ||||||||||||
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 / FOURIER SYNTHESIS / Resolution: 1.65 Å | ||||||||||||
Authors | Schneider, S. / Gross, O. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: To Be Published Title: Imiquimod Inhibits Mitochondrial Complex I and Induces K+ efflux-independent Nlrp3 Inflammasome Activation via Nek7 Authors: Gross, C. / Mishra, R. / Schneider, K. / Medard, G. / Wettmarshausen, J. / Dittlein, D. / Gorka, O. / Koenig, P.-A. / Fromm, S. / Magnani, G. / Cikovic, T. / Hartjes, L. / Smollich, J. / ...Authors: Gross, C. / Mishra, R. / Schneider, K. / Medard, G. / Wettmarshausen, J. / Dittlein, D. / Gorka, O. / Koenig, P.-A. / Fromm, S. / Magnani, G. / Cikovic, T. / Hartjes, L. / Smollich, J. / Robertson, A. / Cooper, M. / Schmidt-Supprian, M. / Schuster, M. / Schroder, K. / Broz, P. / Traidl-Hoffmann, C. / Kuester, B. / Ruland, J. / Schneider, S. / Perocchi, F. / Gross, O. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lbu.cif.gz | 117.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lbu.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 5lbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/5lbu ftp://data.pdbj.org/pub/pdb/validation_reports/lb/5lbu | HTTPS FTP |
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-Related structure data
Related structure data | 5lbtC 2bzsS S: Starting model for refinement 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 26775.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P16083, ribosyldihydronicotinamide dehydrogenase (quinone) |
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-Non-polymers , 5 types, 274 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-C09 / #6: 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: 2.31 Å3/Da / Density % sol: 46.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.1 M Tris HCl pH 8.5 2 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→44.3 Å / Num. obs: 59424 / % possible obs: 99 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.42 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 0.9 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2BZS Resolution: 1.65→44.3 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.98 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.095 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.614 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→44.3 Å
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