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- PDB-8t7d: Crystal structure of wild type IDH1 bound to compound 1 -

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Basic information

Entry
Database: PDB / ID: 8t7d
TitleCrystal structure of wild type IDH1 bound to compound 1
ComponentsIsocitrate dehydrogenase [NADP] cytoplasmic
KeywordsOXIDOREDUCTASE
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 / NADP+ metabolic process / 2-oxoglutarate 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 / NADP+ metabolic process / 2-oxoglutarate 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 / cytosol / cytoplasm
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase
Similarity search - Domain/homology
: / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.444 Å
AuthorsLu, J. / Abeywickrema, P. / Heo, M.R. / Parthasarathy, G. / McCoy, M. / Soisson, S.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Biostructural, biochemical and biophysical studies of mutant IDH1.
Authors: McCoy, M.A. / Lu, J. / Richard Miller, F. / Soisson, S.M. / Lam, M.H. / Fischer, C.
History
DepositionJun 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)193,8738
Polymers192,2714
Non-polymers1,6024
Water00
1
A: Isocitrate dehydrogenase [NADP] cytoplasmic
B: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9364
Polymers96,1352
Non-polymers8012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-37 kcal/mol
Surface area33580 Å2
MethodPISA
2
C: Isocitrate dehydrogenase [NADP] cytoplasmic
D: Isocitrate dehydrogenase [NADP] cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9364
Polymers96,1352
Non-polymers8012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-38 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.592, 120.991, 139.274
Angle α, β, γ (deg.)90, 119.39, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Isocitrate dehydrogenase [NADP] cytoplasmic / IDH / IDH1 / Cytosolic NADP-isocitrate dehydrogenase / IDPc / NADP(+)-specific ICDH / ...IDH / IDH1 / Cytosolic NADP-isocitrate dehydrogenase / IDPc / NADP(+)-specific ICDH / Oxalosuccinate decarboxylase


Mass: 48067.652 Da / Num. of mol.: 4
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-ZT3 / N-(4-tert-butylphenyl)-7,8-dimethyl-5,11-dihydro-6H-pyrido[2,3-b][1,5]benzodiazepine-6-carboxamide


Mass: 400.516 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H28N4O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium Cacodylate, pH6.5, 0.2M NaCl, 2M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.44→121.35 Å / Num. obs: 30579 / % possible obs: 99.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.6
Reflection shellResolution: 3.44→3.63 Å / Rmerge(I) obs: 0.455 / Num. unique obs: 4446

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.444→91.52 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.849 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.546
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 1536 -RANDOM
Rwork0.2405 ---
obs0.2418 30571 98.9 %-
Displacement parametersBiso mean: 88.73 Å2
Baniso -1Baniso -2Baniso -3
1--15.0322 Å20 Å28.7379 Å2
2--7.3929 Å20 Å2
3---7.6393 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: LAST / Resolution: 3.444→91.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11533 0 120 0 11653
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00811914HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9916265HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3754SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2089HARMONIC8
X-RAY DIFFRACTIONt_it11782HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1658SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8157SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion1.6
X-RAY DIFFRACTIONt_other_torsion20.57
LS refinement shellResolution: 3.444→3.47 Å
RfactorNum. reflection% reflection
Rfree0.3237 25 -
Rwork0.2985 --
obs--99.51 %

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