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Open data
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Basic information
Entry | Database: PDB / ID: 6adg | ||||||
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Title | Crystal Structures of IDH1 R132H in complex with AG-881 | ||||||
![]() | Isocitrate dehydrogenase [NADP] cytoplasmic | ||||||
![]() | OXIDOREDUCTASE / IDH1 | ||||||
Function / homology | ![]() Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / regulation of phospholipid catabolic process / NADPH regeneration / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process ...Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / regulation of phospholipid catabolic process / NADPH regeneration / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / response to steroid hormone / female gonad development / peroxisomal matrix / tricarboxylic acid cycle / glutathione metabolic process / Peroxisomal protein import / NAD binding / tertiary granule lumen / peroxisome / NADP binding / secretory granule lumen / response to oxidative stress / ficolin-1-rich granule lumen / cadherin binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ma, R. / Yun, C.H. | ||||||
![]() | ![]() Title: Crystal structures of pan-IDH inhibitor AG-881 in complex with mutant human IDH1 and IDH2 Authors: Ma, R. / Yun, C.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 248.8 KB | Display | ![]() |
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PDB format | ![]() | 198.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6adiC ![]() 5de1S 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 48135.684 Da / Num. of mol.: 3 / Mutation: R132H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O75874, isocitrate dehydrogenase (NADP+) #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M Magnesium chloride hexahydrate, 0.1M Tris pH 8.5, 25%(w/v) Polyethylene glycol 3,350, 0.1M Cesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 30674 / % possible obs: 92.6 % / Redundancy: 3.8 % / Rpim(I) all: 0.105 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 3→3.23 Å / Num. unique obs: 5478 / Rpim(I) all: 0.436 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DE1 Resolution: 3→43.015 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 24.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→43.015 Å
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Refine LS restraints |
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LS refinement shell |
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