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Yorodumi- PDB-2h5l: S-Adenosylhomocysteine hydrolase containing NAD and 3-deaza-D-eri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h5l | ||||||
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Title | S-Adenosylhomocysteine hydrolase containing NAD and 3-deaza-D-eritadenine | ||||||
Components | Adenosylhomocysteinase | ||||||
Keywords | HYDROLASE / S-Adenosylhomocysteine / Inhibitor / Hypocholesterolemic activity | ||||||
Function / homology | Function and homology information adenosylselenohomocysteinase activity / S-adenosylhomocysteine catabolic process / Sulfur amino acid metabolism / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / adenosylhomocysteinase / S-adenosylmethionine cycle / adenosylhomocysteinase activity / Methylation ...adenosylselenohomocysteinase activity / S-adenosylhomocysteine catabolic process / Sulfur amino acid metabolism / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / adenosylhomocysteinase / S-adenosylmethionine cycle / adenosylhomocysteinase activity / Methylation / response to nutrient / NAD binding / : / melanosome / one-carbon metabolic process / response to hypoxia / copper ion binding / endoplasmic reticulum / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Yamada, T. / Komoto, J. / Takusagawa, F. | ||||||
Citation | Journal: Biochem.Pharm. / Year: 2007 Title: Structure and function of eritadenine and its 3-deaza analogues: Potent inhibitors of S-adenosylhomocysteine hydrolase and hypocholesterolemic agents. Authors: Yamada, T. / Komoto, J. / Lou, K. / Ueki, A. / Hua, D.H. / Sugiyama, K. / Takata, Y. / Ogawa, H. / Takusagawa, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h5l.cif.gz | 635.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h5l.ent.gz | 526.4 KB | Display | PDB format |
PDBx/mmJSON format | 2h5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/2h5l ftp://data.pdbj.org/pub/pdb/validation_reports/h5/2h5l | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47465.711 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ahcy / Production host: Escherichia coli (E. coli) / References: UniProt: P10760, adenosylhomocysteinase #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-3DD / ( #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: 2.28 Å3/Da / Density % sol: 46.07 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6.5 Details: 15% PGE-8000, 50 mM MES, 2% glycerol, pH 6.5, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 78969 / Num. obs: 78969 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 80.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.034 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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