+Open data
-Basic information
Entry | Database: PDB / ID: 5svo | ||||||
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Title | Structure of IDH2 mutant R140Q | ||||||
Components | Isocitrate dehydrogenase [NADP], mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / inhibitor / isocitrate dehydrogenase / MITOCHONDRIAL / NADPH | ||||||
Function / homology | Function and homology information 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 / Transcriptional activation of mitochondrial biogenesis / peroxisome ...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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.87 Å | ||||||
Authors | Xie, X. / Kulathila, R. | ||||||
Citation | Journal: Structure / Year: 2017 Title: Allosteric Mutant IDH1 Inhibitors Reveal Mechanisms for IDH1 Mutant and Isoform Selectivity. Authors: Xie, X. / Baird, D. / Bowen, K. / Capka, V. / Chen, J. / Chenail, G. / Cho, Y. / Dooley, J. / Farsidjani, A. / Fortin, P. / Kohls, D. / Kulathila, R. / Lin, F. / McKay, D. / Rodrigues, L. / ...Authors: Xie, X. / Baird, D. / Bowen, K. / Capka, V. / Chen, J. / Chenail, G. / Cho, Y. / Dooley, J. / Farsidjani, A. / Fortin, P. / Kohls, D. / Kulathila, R. / Lin, F. / McKay, D. / Rodrigues, L. / Sage, D. / Toure, B.B. / van der Plas, S. / Wright, K. / Xu, M. / Yin, H. / Levell, J. / Pagliarini, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5svo.cif.gz | 338.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5svo.ent.gz | 275.3 KB | Display | PDB format |
PDBx/mmJSON format | 5svo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/5svo ftp://data.pdbj.org/pub/pdb/validation_reports/sv/5svo | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48086.742 Da / Num. of mol.: 2 / Mutation: R140Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDH2 / Production host: Escherichia coli (E. coli) References: UniProt: P48735, isocitrate dehydrogenase (NADP+) #2: Chemical | #3: Chemical | ChemComp-EPE / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 0.1M Hepes pH7.5, 0.2M NaCl, 25% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→127.5 Å / Num. obs: 75021 / % possible obs: 99.9 % / Redundancy: 6.6 % / Net I/σ(I): 25.6 |
Reflection shell | Highest resolution: 1.87 Å |
-Processing
Software |
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Refinement | Resolution: 1.87→87.08 Å / Cor.coef. Fo:Fc: 0.9559 / Cor.coef. Fo:Fc free: 0.9458 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.139 / SU Rfree Blow DPI: 0.125 / SU Rfree Cruickshank DPI: 0.123
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Displacement parameters | Biso mean: 49.43 Å2
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Refine analyze | Luzzati coordinate error obs: 0.235 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.87→87.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.92 Å / Total num. of bins used: 20
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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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