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- PDB-6adi: Crystal Structures of IDH2 R140Q in complex with AG-881 -

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Basic information

Entry
Database: PDB / ID: 6adi
TitleCrystal Structures of IDH2 R140Q in complex with AG-881
ComponentsIsocitrate dehydrogenase [NADP], mitochondrial
KeywordsOXIDOREDUCTASE
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 / Mitochondrial protein degradation / tricarboxylic acid cycle / Transcriptional activation of mitochondrial biogenesis ...Citric acid cycle (TCA cycle) / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / Mitochondrial protein degradation / 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
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-9UO / Chem-NDP / Isocitrate dehydrogenase [NADP], mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.969 Å
AuthorsMa, R. / Yun, C.H.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structures of pan-IDH inhibitor AG-881 in complex with mutant human IDH1 and IDH2
Authors: Ma, R. / Yun, C.H.
History
DepositionAug 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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], mitochondrial
B: Isocitrate dehydrogenase [NADP], mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9885
Polymers95,0822
Non-polymers1,9063
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-63 kcal/mol
Surface area33350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.781, 118.419, 126.082
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isocitrate dehydrogenase [NADP], mitochondrial / IDH / ICD-M / IDP / NADP(+)-specific ICDH / Oxalosuccinate decarboxylase


Mass: 47541.223 Da / Num. of mol.: 2 / Fragment: UNP residues 41-452 / Mutation: R140Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDH2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P48735, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-9UO / 6-(6-chloropyridin-2-yl)-N2,N4-bis[(2R)-1,1,1-trifluoropropan-2-yl]-1,3,5-triazine-2,4-diamine


Mass: 414.737 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13ClF6N6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium chloride, 0.1M BIS-TRIS pH 6.5, 25%(w/v) Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 64048 / % possible obs: 96.7 % / Redundancy: 6.4 % / Rpim(I) all: 0.037 / Net I/σ(I): 22.3
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 3936 / Rpim(I) all: 0.281

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DENZOdata reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I96

5i96


Resolution: 1.969→39.607 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.24
RfactorNum. reflection% reflection
Rfree0.2264 3089 5.06 %
Rwork0.2058 --
obs0.2069 61010 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.969→39.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6529 0 123 468 7120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0186881
X-RAY DIFFRACTIONf_angle_d1.6619341
X-RAY DIFFRACTIONf_dihedral_angle_d21.1492492
X-RAY DIFFRACTIONf_chiral_restr0.3731012
X-RAY DIFFRACTIONf_plane_restr0.011184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9694-2.00020.2542960.23762063X-RAY DIFFRACTION77
2.0002-2.0330.27941570.24252447X-RAY DIFFRACTION94
2.033-2.0680.27021530.24172559X-RAY DIFFRACTION97
2.068-2.10560.24421500.23172595X-RAY DIFFRACTION99
2.1056-2.14610.27761330.23062674X-RAY DIFFRACTION100
2.1461-2.18990.26131600.21712593X-RAY DIFFRACTION100
2.1899-2.23760.2591120.21862686X-RAY DIFFRACTION100
2.2376-2.28960.25841300.21632641X-RAY DIFFRACTION100
2.2896-2.34690.26651360.21972635X-RAY DIFFRACTION100
2.3469-2.41030.24111420.22242673X-RAY DIFFRACTION100
2.4103-2.48120.27571250.22622656X-RAY DIFFRACTION100
2.4812-2.56130.27711390.22092656X-RAY DIFFRACTION100
2.5613-2.65280.24081420.20862656X-RAY DIFFRACTION100
2.6528-2.7590.22261470.20982684X-RAY DIFFRACTION100
2.759-2.88450.22991510.20952656X-RAY DIFFRACTION100
2.8845-3.03660.23121490.21922653X-RAY DIFFRACTION100
3.0366-3.22670.24141360.212702X-RAY DIFFRACTION100
3.2267-3.47570.21411620.19722656X-RAY DIFFRACTION100
3.4757-3.82530.20411240.18632728X-RAY DIFFRACTION100
3.8253-4.37820.17971340.17332733X-RAY DIFFRACTION100
4.3782-5.51370.17711540.17472731X-RAY DIFFRACTION100
5.5137-39.61490.19531570.20632844X-RAY DIFFRACTION99

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