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Yorodumi- PDB-1wpq: Ternary Complex Of Glycerol 3-phosphate Dehydrogenase 1 with NAD ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wpq | ||||||
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Title | Ternary Complex Of Glycerol 3-phosphate Dehydrogenase 1 with NAD and dihydroxyactone | ||||||
Components | Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic | ||||||
Keywords | OXIDOREDUCTASE / NAD / GPD1 / DEHYDROGENASE / DIHYDROXYACTONE COMPLEX | ||||||
Function / homology | Function and homology information glycerophosphate shuttle / glycerolipid metabolic process / glycerol-3-phosphate dehydrogenase (quinone) activity / glycerol-3-phosphate dehydrogenase [NAD(P)+] activity / glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate catabolic process / glycerol-3-phosphate dehydrogenase (FAD) complex / NADH oxidation / glycerol-3-phosphate metabolic process / Synthesis of PA ...glycerophosphate shuttle / glycerolipid metabolic process / glycerol-3-phosphate dehydrogenase (quinone) activity / glycerol-3-phosphate dehydrogenase [NAD(P)+] activity / glycerol-3-phosphate dehydrogenase (NAD+) / glycerol-3-phosphate catabolic process / glycerol-3-phosphate dehydrogenase (FAD) complex / NADH oxidation / glycerol-3-phosphate metabolic process / Synthesis of PA / NADH metabolic process / cellular response to cAMP / positive regulation of glycolytic process / gluconeogenesis / NAD binding / cellular response to tumor necrosis factor / protein homodimerization activity / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Ou, X. / Han, X. / Rao, Z. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Crystal Structures of Human Glycerol 3-phosphate Dehydrogenase 1 (GPD1) Authors: Ou, X. / Ji, C. / Han, X. / Zhao, X. / Li, X. / Mao, Y. / Wong, L.L. / Bartlam, M. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wpq.cif.gz | 140.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wpq.ent.gz | 108.2 KB | Display | PDB format |
PDBx/mmJSON format | 1wpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/1wpq ftp://data.pdbj.org/pub/pdb/validation_reports/wp/1wpq | 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
#1: Protein | Mass: 37634.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P21695, glycerol-3-phosphate dehydrogenase (NAD+) #2: Chemical | ChemComp-SO4 / #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: 3.5 Å3/Da / Density % sol: 64.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: tri-sodium Citrate dehydrate, Ammonium Sulfate, Lithium Sulfate monohydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2004 / Details: mirror |
Radiation | Monochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→500 Å / Num. all: 73285 / Num. obs: 73285 |
Reflection shell | Resolution: 2.45→2.54 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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