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- PDB-5gri: Crystal structure of the alpha gamma heterodimer of human IDH3 in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gri | ||||||||||||
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Title | Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+) and citrate | ||||||||||||
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![]() | OXIDOREDUCTASE / allosteric regulation | ||||||||||||
Function / homology | ![]() : / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / Mitochondrial protein import / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process ...: / isocitrate dehydrogenase (NAD+) / isocitrate dehydrogenase (NAD+) activity / Citric acid cycle (TCA cycle) / isocitrate metabolic process / Mitochondrial protein import / tricarboxylic acid cycle / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / mitochondrial matrix / nucleolus / magnesium ion binding / mitochondrion / ATP binding / nucleus Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Ma, T. / Peng, Y. / Ding, J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanism of the allosteric regulation of the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase. Authors: Ma, T. / Peng, Y. / Huang, W. / Ding, J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.4 KB | Display | ![]() |
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PDB format | ![]() | 109.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.4 KB | Display | ![]() |
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Full document | ![]() | 463.3 KB | Display | |
Data in XML | ![]() | 25.4 KB | Display | |
Data in CIF | ![]() | 35.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5greC ![]() 5grfC ![]() 5grhSC ![]() 5grlC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 36682.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P50213, isocitrate dehydrogenase (NAD+) | ||||
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#2: Protein | Mass: 38867.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P51553, isocitrate dehydrogenase (NAD+) | ||||
#3: Chemical | #4: Chemical | ChemComp-CIT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M sodium citrate, pH 8.0, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 46471 / % possible obs: 98.4 % / Redundancy: 19.5 % / Net I/σ(I): 53.7 |
Reflection shell | Resolution: 2.3→2.38 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5GRH Resolution: 2.31→46.01 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.886 / SU B: 5.499 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.05 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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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 max: 134.01 Å2 / Biso mean: 44.364 Å2 / Biso min: 7.81 Å2
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Refinement step | Cycle: final / Resolution: 2.31→46.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.305→2.365 Å / Total num. of bins used: 20
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