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Yorodumi- PDB-4gqi: Synthesis of novel MT3 receptor ligands via unusual Knoevenagel c... -
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-Basic information
Entry | Database: PDB / ID: 4gqi | ||||||
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Title | Synthesis of novel MT3 receptor ligands via unusual Knoevenagel condensation | ||||||
Components | Ribosyldihydronicotinamide dehydrogenase [quinone] | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.948 Å | ||||||
Authors | Volkova, M.S. / Jensen, K.C. / Lozinskaya, N.A. / Sosonyuk, S.E. / Proskurnina, M.V. / Mesecar, A.D. / Zefirov, N.S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2012 Title: Synthesis of novel МТ3 receptor ligands via an unusual Knoevenagel condensation. Authors: Volkova, M.S. / Jensen, K.C. / Lozinskaya, N.A. / Sosonyuk, S.E. / Proskurnina, M.V. / Mesecar, A.D. / Zefirov, N.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gqi.cif.gz | 202.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gqi.ent.gz | 161.9 KB | Display | PDB format |
PDBx/mmJSON format | 4gqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/4gqi ftp://data.pdbj.org/pub/pdb/validation_reports/gq/4gqi | HTTPS FTP |
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-Related 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: 25849.338 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NQO2, NMOR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P16083, EC: 1.10.99.2 |
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-Non-polymers , 5 types, 217 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | L47F IS A NATURAL VARIANT. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.29 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
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Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.948→25.688 Å / Num. all: 36364 / Num. obs: 36186 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.948→25.688 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.547 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.143 / 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 max: 68.79 Å2 / Biso mean: 30.973 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.948→25.688 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.948→1.999 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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