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Yorodumi- PDB-5i95: Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase... -
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-Basic information
Entry | Database: PDB / ID: 5i95 | ||||||
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Title | Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Homodimer bound to NADPH and alpha-Ketoglutaric acid | ||||||
Components | Isocitrate dehydrogenase [NADP], mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / IDH / ICD-M / IDP NADP(+)-specific ICDH Oxalosuccinate decarboxylase / aKG / alphaKG / oxo-glutarate. | ||||||
Function / homology | Function and homology information Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of 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 ...Citric acid cycle (TCA cycle) / Maturation of TCA enzymes and regulation of 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 / NAD binding / peroxisome / carbohydrate metabolic process / mitochondrial matrix / magnesium ion binding / mitochondrion / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Zhang, B. / Jin, L. / Wu, W. / Jiang, F. / DeLaBarre, B. / Travins, J.A. / Padyana, A.K. | ||||||
Citation | Journal: Cancer Discov / Year: 2017 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: Journal: Science / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i95.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i95.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 5i95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5i95_validation.pdf.gz | 830.4 KB | Display | wwPDB validaton report |
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Full document | 5i95_full_validation.pdf.gz | 837.7 KB | Display | |
Data in XML | 5i95_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 5i95_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/5i95 ftp://data.pdbj.org/pub/pdb/validation_reports/i9/5i95 | HTTPS FTP |
-Related structure data
Related structure data | 5i96C 4ja8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48130.855 Da / Num. of mol.: 1 / Fragment: UNP residues 40-452 / Mutation: R140Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDH2 / Plasmid: pET-41a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P48735, isocitrate dehydrogenase (NADP+) |
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-Non-polymers , 6 types, 597 molecules
#2: Chemical | ChemComp-NDP / | ||||||
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#3: Chemical | ChemComp-CA / | ||||||
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ACT / | #6: Chemical | ChemComp-AKG / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 200 mM magnesium acetate, 100 mM sodium cacodylate, pH 6.5, 20% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.54→29.83 Å / Num. obs: 72657 / % possible obs: 99.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.078 / Χ2: 1.054 / Net I/av σ(I): 19.495 / Net I/σ(I): 10.5 / Num. measured all: 350607 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JA8 Resolution: 1.54→29.83 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.243 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.4 Å2 / Biso mean: 17.449 Å2 / Biso min: 4.28 Å2
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Refinement step | Cycle: final / Resolution: 1.54→29.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.54→1.58 Å / Total num. of bins used: 20
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