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- PDB-5i96: Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5i96 | ||||||
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Title | Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with AG-221 (Enasidenib) Inhibitor. | ||||||
![]() | Isocitrate dehydrogenase [NADP], mitochondrial | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / IDH / IDH2 / enasidenib / AG-221 / IDH2 AG-221 / ICD-M / IDP NADP(+)-specific ICDH Oxalosuccinate decarboxylase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | ![]() Citric acid cycle (TCA cycle) / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / tricarboxylic acid cycle / Mitochondrial protein degradation / Transcriptional activation of mitochondrial biogenesis ...Citric acid cycle (TCA cycle) / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / tricarboxylic acid cycle / Mitochondrial protein degradation / Transcriptional activation of mitochondrial biogenesis / peroxisome / NAD binding / carbohydrate metabolic process / mitochondrial matrix / magnesium ion binding / mitochondrion / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wei, W. / Zhang, B. / Jin, L. / Jiang, F. / DeLaBarre, B. / Travins, J.A. / Padyana, A.K. | ||||||
![]() | ![]() Title: AG-221, a First-in-Class Therapy Targeting Acute Myeloid Leukemia Harboring Oncogenic IDH2 Mutations. Authors: Yen, K. / Travins, J. / Wang, F. / David, M.D. / Artin, E. / Straley, K. / Padyana, A. / Gross, S. / DeLaBarre, B. / Tobin, E. / Chen, Y. / Nagaraja, R. / Choe, S. / Jin, L. / Konteatis, Z. ...Authors: Yen, K. / Travins, J. / Wang, F. / David, M.D. / Artin, E. / Straley, K. / Padyana, A. / Gross, S. / DeLaBarre, B. / Tobin, E. / Chen, Y. / Nagaraja, R. / Choe, S. / Jin, L. / Konteatis, Z. / Cianchetta, G. / Saunders, J.O. / Salituro, F.G. / Quivoron, C. / Opolon, P. / Bawa, O. / Saada, V. / Paci, A. / Broutin, S. / Bernard, O.A. / de Botton, S. / Marteyn, B.S. / Pilichowska, M. / Xu, Y. / Fang, C. / Jiang, F. / Wei, W. / Jin, S. / Silverman, L. / Liu, W. / Yang, H. / Dang, L. / Dorsch, M. / Penard-Lacronique, V. / Biller, S.A. / Su, S.M. #1: ![]() Title: Targeted inhibition of mutant IDH2 in leukemia cells induces cellular differentiation. Authors: Wang, F. / Travins, J. / DeLaBarre, B. / Penard-Lacronique, V. / Schalm, S. / Hansen, E. / Straley, K. / Kernytsky, A. / Liu, W. / Gliser, C. / Yang, H. / Gross, S. / Artin, E. / Saada, V. / ...Authors: Wang, F. / Travins, J. / DeLaBarre, B. / Penard-Lacronique, V. / Schalm, S. / Hansen, E. / Straley, K. / Kernytsky, A. / Liu, W. / Gliser, C. / Yang, H. / Gross, S. / Artin, E. / Saada, V. / Mylonas, E. / Quivoron, C. / Popovici-Muller, J. / Saunders, J.O. / Salituro, F.G. / Yan, S. / Murray, S. / Wei, W. / Gao, Y. / Dang, L. / Dorsch, M. / Agresta, S. / Schenkein, D.P. / Biller, S.A. / Su, S.M. / de Botton, S. / Yen, K.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 387.5 KB | Display | ![]() |
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PDB format | ![]() | 314.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 43.9 KB | Display | |
Data in CIF | ![]() | 66.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i95C ![]() 4ja8S 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 51783.008 Da / Num. of mol.: 2 / Mutation: R140Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P48735, isocitrate dehydrogenase (NADP+) |
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-Non-polymers , 7 types, 993 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/69Q.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/69Q.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-69Q / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, pH 8.5, 0.25 M CaCl2, 25% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→48.4 Å / Num. obs: 121589 / % possible obs: 95 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.028 / Rrim(I) all: 0.059 / Χ2: 1.078 / Net I/av σ(I): 24.353 / Net I/σ(I): 12.5 / Num. measured all: 543881 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JA8 Resolution: 1.55→41.896 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→41.896 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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