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- PDB-5sun: IDH1 R132H in complex with IDH146 -

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Basic information

Entry
Database: PDB / ID: 5sun
TitleIDH1 R132H in complex with IDH146
ComponentsIsocitrate dehydrogenase [NADP] cytoplasmic
KeywordsOXIDOREDUCTASE / inhibitor / isocitrate dehydrogenase / NADPH
Function / homology
Function and homology information


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 / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process ...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 / 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 / peroxisome / NAD binding / tertiary granule lumen / NADP binding / secretory granule lumen / ficolin-1-rich granule lumen / response to oxidative stress / cadherin binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-70Q / Chem-NDP / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.477 Å
AuthorsXie, X. / Kulathila, R.
CitationJournal: 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
DepositionAug 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isocitrate dehydrogenase [NADP] cytoplasmic
B: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,90514
Polymers93,8252
Non-polymers3,08112
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-89 kcal/mol
Surface area34740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.563, 82.563, 302.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Isocitrate dehydrogenase [NADP] cytoplasmic / IDH / Cytosolic NADP-isocitrate dehydrogenase / IDP / NADP(+)-specific ICDH / Oxalosuccinate decarboxylase


Mass: 46912.391 Da / Num. of mol.: 2 / 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+)

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Non-polymers , 6 types, 92 molecules

#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-70Q / 3-benzyl-N-[3-(dimethylsulfamoyl)phenyl]-4-oxo-3,4-dihydrophthalazine-1-carboxamide


Mass: 462.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H22N4O4S
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5 / Details: 27% PEG3350, 0.22M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.477→72.472 Å / Num. obs: 38566 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 56.53 Å2 / Rsym value: 0.06 / Net I/av σ(I): 9.678 / Net I/σ(I): 28.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.48-2.6112.90.5711.31100
2.61-2.7713.20.3462.21100
2.77-2.9613.30.2223.41100
2.96-3.212.60.1395.41100
3.2-3.512.50.0838.81100
3.5-3.9212.30.057121100
3.92-4.5211.60.04613.61100
4.52-5.5412.30.03915.61100
5.54-7.8311.80.03517.41100
7.83-72.4710.90.02324.6199.7

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.477→63.88 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.29
RfactorNum. reflection% reflection
Rfree0.2213 1925 5.01 %
Rwork0.1904 --
obs0.1919 38450 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.31 Å2 / Biso mean: 59.0871 Å2 / Biso min: 36.36 Å2
Refinement stepCycle: final / Resolution: 2.477→63.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6171 0 198 80 6449
Biso mean--67.44 56.73 -
Num. residues----778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056500
X-RAY DIFFRACTIONf_angle_d0.6628779
X-RAY DIFFRACTIONf_chiral_restr0.046948
X-RAY DIFFRACTIONf_plane_restr0.0031094
X-RAY DIFFRACTIONf_dihedral_angle_d19.3613843
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4765-2.53840.3271310.242325662697
2.5384-2.60710.30521440.23525332677
2.6071-2.68380.26181370.217625622699
2.6838-2.77040.26251380.212825582696
2.7704-2.86940.29371310.217225502681
2.8694-2.98430.27981360.225725742710
2.9843-3.12020.25951300.224625762706
3.1202-3.28470.23011420.202725782720
3.2847-3.49040.24051470.194925812728
3.4904-3.75990.21991240.188226392763
3.7599-4.13830.19541480.173826032751
4.1383-4.7370.18551460.157226302776
4.737-5.96770.19871450.181626942839
5.9677-72.50280.20911260.190628813007

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