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- PDB-6vg0: CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC ISOCITRATE DEHYDROGENASE (ID... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vg0 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC ISOCITRATE DEHYDROGENASE (IDH1) R132H MUTANT IN COMPLEX WITH NADPH and AGI-15056 | ||||||
![]() | Isocitrate dehydrogenase [NADP] cytoplasmic | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / IDH / CYTOSOLIC NADP-ISOCITRATE DEHYDROGENASE / OXALOSUCCINATE DECARBOXYLASE / NADP(+)-SPECIFIC ICDH / IDP / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex | ||||||
Function / homology | ![]() Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / NADPH regeneration / regulation of phospholipid catabolic process / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Padyana, A. / Jin, L. | ||||||
![]() | ![]() Title: Vorasidenib (AG-881): A First-in-Class, Brain-Penetrant Dual Inhibitor of Mutant IDH1 and 2 for Treatment of Glioma. Authors: Konteatis, Z. / Artin, E. / Nicolay, B. / Straley, K. / Padyana, A.K. / Jin, L. / Chen, Y. / Narayaraswamy, R. / Tong, S. / Wang, F. / Zhou, D. / Cui, D. / Cai, Z. / Luo, Z. / Fang, C. / ...Authors: Konteatis, Z. / Artin, E. / Nicolay, B. / Straley, K. / Padyana, A.K. / Jin, L. / Chen, Y. / Narayaraswamy, R. / Tong, S. / Wang, F. / Zhou, D. / Cui, D. / Cai, Z. / Luo, Z. / Fang, C. / Tang, H. / Lv, X. / Nagaraja, R. / Yang, H. / Su, S.M. / Sui, Z. / Dang, L. / Yen, K. / Popovici-Muller, J. / Codega, P. / Campos, C. / Mellinghoff, I.K. / Biller, S.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 319.3 KB | Display | ![]() |
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PDB format | ![]() | 210.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6veiC ![]() 6vfzC ![]() 3inmS C: citing same article ( S: Starting model for refinement |
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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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: O75874, ![]() #2: Chemical | ![]() #3: Chemical | #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.38 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.25 M ammonium sulfate, 0.1M sodium citrate pH 5.6, 23% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.66→41.2 Å / Num. obs: 45671 / % possible obs: 98.1 % / Redundancy: 5 % / Biso Wilson estimate: 42.85 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.66→2.73 Å / Rmerge(I) obs: 0.694 / Num. unique obs: 3370 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3INM Resolution: 2.66→41.2 Å / SU ML: 0.4066 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.4807 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.66→41.2 Å
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Refine LS restraints |
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LS refinement shell |
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