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- PDB-9m82: Crystal Structure of Human IDH1 in Complex with Kinsenoside -

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Basic information

Entry
Database: PDB / ID: 9m82
TitleCrystal Structure of Human IDH1 in Complex with Kinsenoside
ComponentsIsocitrate dehydrogenase [NADP] cytoplasmic
KeywordsOXIDOREDUCTASE / IDH1 / Complex / IsoCltrate dehydrogenase
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+) / NADPH regeneration / isocitrate dehydrogenase (NADP+) activity / 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+) / NADPH regeneration / 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 / NADP binding / tertiary granule lumen / peroxisome / response to oxidative stress / secretory granule lumen / ficolin-1-rich granule lumen / 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 / 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: 3.08 Å
AuthorsOuyang, S. / Zhao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82172287 China
CitationJournal: To Be Published
Title: Crystal Structure of Human IDH1 in Complex with Kinsenoside
Authors: Ouyang, S.
History
DepositionMar 11, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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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)100,1764
Polymers99,6472
Non-polymers5282
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-52 kcal/mol
Surface area32420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.899, 112.379, 97.766
Angle α, β, γ (deg.)90.00, 91.88, 90.00
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: 49823.672 Da / Num. of mol.: 2
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-A1EOQ / Kinsenoside / (4R)-4-[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxolan-2-one


Mass: 264.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O8 / 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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.5 M Ammonium Sulfate; 0.1 M Mes, pH6.0 15% PEG4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.08→56.19 Å / Num. obs: 19054 / % possible obs: 92.41 % / Redundancy: 6.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.4
Reflection shellResolution: 3.08→3.19 Å / Num. unique obs: 19054 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.08→56.19 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3008 1750 9.93 %
Rwork0.2506 --
obs0.2556 17626 92.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.08→56.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6514 0 36 0 6550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046688
X-RAY DIFFRACTIONf_angle_d0.8649022
X-RAY DIFFRACTIONf_dihedral_angle_d18.2352472
X-RAY DIFFRACTIONf_chiral_restr0.051980
X-RAY DIFFRACTIONf_plane_restr0.0071154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.160.36561160.34721060X-RAY DIFFRACTION81
3.16-3.260.33941320.32241123X-RAY DIFFRACTION86
3.26-3.360.36491230.30361146X-RAY DIFFRACTION86
3.36-3.480.38061170.32061179X-RAY DIFFRACTION90
3.48-3.620.3681330.29961229X-RAY DIFFRACTION92
3.62-3.790.32541330.26281229X-RAY DIFFRACTION94
3.79-3.990.28651320.25551273X-RAY DIFFRACTION96
3.99-4.230.28551460.24621250X-RAY DIFFRACTION97
4.23-4.560.29141420.22651279X-RAY DIFFRACTION96
4.56-5.020.29591430.21681284X-RAY DIFFRACTION97
5.02-5.750.2581430.24021280X-RAY DIFFRACTION96
5.75-7.240.35121450.27131303X-RAY DIFFRACTION98
7.24-56.190.22991450.18891241X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 20.1001 Å / Origin y: 4.7326 Å / Origin z: 28.8728 Å
111213212223313233
T0.1885 Å2-0.0236 Å20.0062 Å2-0.2374 Å2-0.0191 Å2--0.1805 Å2
L0.5286 °20.2096 °20.0575 °2-0.8015 °20.1444 °2--0.386 °2
S0.0764 Å °-0.1319 Å °0.0248 Å °0.092 Å °-0.0575 Å °-0.0466 Å °0.0074 Å °-0.0438 Å °0 Å °
Refinement TLS groupSelection details: all

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