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- PDB-6e8z: Binary complex of Human glycerol 3-phosphate dehydrogenase with NAD -
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Open data
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Basic information
Entry | Database: PDB / ID: 6e8z | |||||||||
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Title | Binary complex of Human glycerol 3-phosphate dehydrogenase with NAD | |||||||||
![]() | Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic | |||||||||
![]() | OXIDOREDUCTASE | |||||||||
Function / homology | ![]() 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 metabolic process / glycerol-3-phosphate catabolic process / glycerol-3-phosphate dehydrogenase (FAD) complex / NADH oxidation / 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 metabolic process / glycerol-3-phosphate catabolic process / glycerol-3-phosphate dehydrogenase (FAD) complex / NADH oxidation / Synthesis of PA / 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mydy, L.S. / Gulick, A.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Human Glycerol 3-Phosphate Dehydrogenase: X-ray Crystal Structures That Guide the Interpretation of Mutagenesis Studies. Authors: Mydy, L.S. / Cristobal, J.R. / Katigbak, R.D. / Bauer, P. / Reyes, A.C. / Kamerlin, S.C.L. / Richard, J.P. / Gulick, A.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 256.1 KB | Display | ![]() |
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PDB format | ![]() | 207.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 986 KB | Display | ![]() |
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Full document | ![]() | 995.1 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6e8yC ![]() 6e90C ![]() 1x0xS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37608.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P21695, glycerol-3-phosphate dehydrogenase (NAD+) |
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-Non-polymers , 5 types, 240 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.89 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 200 mM potassium chloride, 23% PEG 20000, 0.1 M bis-tris propane pH 7.0, 10 mM NAD; 10 mg/mL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→33.96 Å / Num. obs: 37384 / % possible obs: 96.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.056 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.195 / Num. unique obs: 3740 / CC1/2: 0.966 / Rrim(I) all: 0.234 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1X0X Resolution: 2.1→33.96 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.07 / Phase error: 25.73
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→33.96 Å
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Refine LS restraints |
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LS refinement shell |
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