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- PDB-6bl0: Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modif... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bl0 | ||||||
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Title | Novel Modes of Inhibition of Wild-Type IDH1:Direct Covalent Modification of His315 with Cmpd11 | ||||||
![]() | Isocitrate dehydrogenase [NADP] cytoplasmic | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / ![]() ![]() ![]() | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Jakob, C.G. / Qiu, W. | ||||||
![]() | ![]() Title: Novel Modes of Inhibition of Wild-Type Isocitrate Dehydrogenase 1 (IDH1): Direct Covalent Modification of His315. Authors: Jakob, C.G. / Upadhyay, A.K. / Donner, P.L. / Nicholl, E. / Addo, S.N. / Qiu, W. / Ling, C. / Gopalakrishnan, S.M. / Torrent, M. / Cepa, S.P. / Shanley, J. / Shoemaker, A.R. / Sun, C.C. / ...Authors: Jakob, C.G. / Upadhyay, A.K. / Donner, P.L. / Nicholl, E. / Addo, S.N. / Qiu, W. / Ling, C. / Gopalakrishnan, S.M. / Torrent, M. / Cepa, S.P. / Shanley, J. / Shoemaker, A.R. / Sun, C.C. / Vasudevan, A. / Woller, K.R. / Shotwell, J.B. / Shaw, B. / Bian, Z. / Hutti, J.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 | ![]() | 274.5 KB | Display | ![]() |
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PDB format | ![]() | 220 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6bkxC ![]() 6bkyC ![]() 6bkzC ![]() 6bl1C ![]() 6bl2C ![]() 4umxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 48154.730 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: O75874, ![]() |
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-Non-polymers , 5 types, 583 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ICT.gif)
![](data/chem/img/DWJ.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ICT.gif)
![](data/chem/img/DWJ.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ![]() #4: Chemical | ChemComp-DWJ / ( | #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.14 % |
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Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion Details: 20% PEG 1500, 0.2M Sodium Chloride, 5% Ethylene Glycol, 0.1M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.165→137.16 Å / Num. obs: 82858 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 50.93 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.165→2.172 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 813 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4UMX Resolution: 2.17→137.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.223 / SU Rfree Blow DPI: 0.177 / SU Rfree Cruickshank DPI: 0.176
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Displacement parameters | Biso mean: 54.54 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.17→137.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.22 Å
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