+Open data
-Basic information
Entry | Database: PDB / ID: 5svf | ||||||
---|---|---|---|---|---|---|---|
Title | IDH1 R132H in complex with IDH125 | ||||||
Components | Isocitrate dehydrogenase [NADP] cytoplasmic | ||||||
Keywords | OXIDOREDUCTASE / Isocitrate dehydrogenase / Rossmann fold / NADPH / inhibitor | ||||||
Function / homology | Function and homology information 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.34 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5svf.cif.gz | 336.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5svf.ent.gz | 272.4 KB | Display | PDB format |
PDBx/mmJSON format | 5svf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5svf_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5svf_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 5svf_validation.xml.gz | 61.1 KB | Display | |
Data in CIF | 5svf_validation.cif.gz | 83.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/5svf ftp://data.pdbj.org/pub/pdb/validation_reports/sv/5svf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 46912.391 Da / Num. of mol.: 4 / Mutation: R132H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDH1, PICD / Production host: Escherichia coli (E. coli) References: UniProt: O75874, isocitrate dehydrogenase (NADP+) #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-70P / ( #4: Chemical | ChemComp-FLC / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.42 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Bis-Tris pH6.5, 1.45M tri-sodium citrate dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→162.99 Å / Num. obs: 88813 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 17.7 |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.34→40.75 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→40.75 Å
|