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- PDB-4umy: IDH1 R132H in complex with cpd 1 -

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Basic information

Entry
Database: PDB / ID: 4umy
TitleIDH1 R132H in complex with cpd 1
ComponentsISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC
KeywordsOXIDOREDUCTASE / ISOCITRATE DEHYDROGENASE INHIBITOR
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 / glutathione metabolic process / tricarboxylic acid cycle / Peroxisomal protein import / peroxisome / NAD binding / tertiary granule lumen / 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 / cytosol / cytoplasm
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsMcLean, L. / Zhang, Y. / Mathieu, M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Selective Inhibition of Mutant Isocitrate Dehydrogenase 1 (Idh1) Via Disruption of a Metal Binding Network by an Allosteric Small Molecule.
Authors: Deng, G. / Shen, J. / Yin, M. / Mcmanus, J. / Mathieu, M. / Gee, P. / He, T. / Shi, C. / Bedel, O. / Mclean, L.R. / Le-Strat, F. / Zhang, Y. / Marquette, J. / Gao, Q. / Zhang, B. / Rak, A. / ...Authors: Deng, G. / Shen, J. / Yin, M. / Mcmanus, J. / Mathieu, M. / Gee, P. / He, T. / Shi, C. / Bedel, O. / Mclean, L.R. / Le-Strat, F. / Zhang, Y. / Marquette, J. / Gao, Q. / Zhang, B. / Rak, A. / Hoffmann, D. / Rooney, E. / Vassort, A. / Englaro, W. / Li, Y. / Patel, V. / Adrian, F. / Gross, S. / Wiederschain, D. / Cheng, H. / Licht, S.
History
DepositionMay 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Mar 29, 2017Group: Other
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)98,2359
Polymers96,2712
Non-polymers1,9637
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-111.9 kcal/mol
Surface area35820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.680, 82.680, 300.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC / IDH / CYTOSOLIC NADP-ISOCITRATE DEHYDROGENASE / IDP / NADP(+)- SPECIFIC ICDH / OXALOSUCCINATE ...IDH / CYTOSOLIC NADP-ISOCITRATE DEHYDROGENASE / IDP / NADP(+)- SPECIFIC ICDH / OXALOSUCCINATE DECARBOXYLASE / IDH1-R132H


Mass: 48135.684 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O75874, isocitrate dehydrogenase (NADP+)
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.8 Å3/Da / Density % sol: 55.79 % / Description: NONE
Crystal growpH: 8
Details: PEG 5000 MME 22% - BIS-TRIS 100MM PH 6.5 - AMMONIUM SULFATE 220 MM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→99.4 Å / Num. obs: 64610 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 44.97 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 31.3
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.36 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T09

1t09


Resolution: 2.07→41.34 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9461 / SU R Cruickshank DPI: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.149 / SU Rfree Cruickshank DPI: 0.148
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 3248 5.06 %RANDOM
Rwork0.2003 ---
obs0.2015 64186 99.16 %-
Displacement parametersBiso mean: 52.14 Å2
Baniso -1Baniso -2Baniso -3
1-3.8202 Å20 Å20 Å2
2--3.8202 Å20 Å2
3----7.6405 Å2
Refine analyzeLuzzati coordinate error obs: 0.264 Å
Refinement stepCycle: LAST / Resolution: 2.07→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6130 0 122 286 6538
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016379HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.048612HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2276SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes161HARMONIC2
X-RAY DIFFRACTIONt_gen_planes937HARMONIC5
X-RAY DIFFRACTIONt_it6379HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion17.52
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion837SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7357SEMIHARMONIC4
LS refinement shellResolution: 2.07→2.12 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2568 193 4.38 %
Rwork0.2343 4212 -
all0.2352 4405 -
obs--99.16 %

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