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- PDB-9vdf: The crystal structure of IDH1 -

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Basic information

Entry
Database: PDB / ID: 9vdf
TitleThe crystal structure of IDH1
ComponentsIsocitrate dehydrogenase [NADP] cytoplasmic
KeywordsOXIDOREDUCTASE / 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+) / 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
: / Chem-NDP / Isocitrate dehydrogenase [NADP] cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, W.H. / Xiao, Q.J. / Qin, W.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The crystal structure of IDH1
Authors: Wang, W.H. / Xiao, Q.J. / Qin, W.M.
History
DepositionJun 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 17, 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)95,1725
Polymers94,0992
Non-polymers1,0733
Water14,286793
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-62 kcal/mol
Surface area33910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.288, 108.581, 100.772
Angle α, β, γ (deg.)90.00, 95.32, 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: 47049.570 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-A1ERX / (1~{R},4~{S},6~{R})-6-oxidanyl-2-(phenylmethyl)-2-azabicyclo[2.2.2]octan-3-one


Mass: 231.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 793 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 277 K / Method: evaporation / Details: 0.2 M Li2SO4, 1M HEPES (pH7.4), and 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→100.34 Å / Num. obs: 83425 / % possible obs: 98.8 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.064 / Rrim(I) all: 0.149 / Χ2: 0.94 / Net I/σ(I): 11.3 / Num. measured all: 410378
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 99.1 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.546 / Num. measured all: 23453 / Num. unique obs: 4595 / CC1/2: 0.583 / Rpim(I) all: 0.261 / Rrim(I) all: 0.607 / Χ2: 0.82 / Net I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→73.5 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 1999 2.4 %
Rwork0.1847 --
obs0.1856 83331 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→73.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6600 0 48 793 7441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086803
X-RAY DIFFRACTIONf_angle_d0.9829187
X-RAY DIFFRACTIONf_dihedral_angle_d7.67909
X-RAY DIFFRACTIONf_chiral_restr0.063991
X-RAY DIFFRACTIONf_plane_restr0.0091173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.29891440.27245838X-RAY DIFFRACTION99
1.95-20.2951420.26395806X-RAY DIFFRACTION99
2-2.060.29731420.24735810X-RAY DIFFRACTION99
2.06-2.130.28881430.22465790X-RAY DIFFRACTION99
2.13-2.20.25151400.20725739X-RAY DIFFRACTION98
2.2-2.290.20961460.18815876X-RAY DIFFRACTION99
2.29-2.390.21331430.18525854X-RAY DIFFRACTION99
2.39-2.520.2311430.18615835X-RAY DIFFRACTION99
2.52-2.680.25041400.19185662X-RAY DIFFRACTION97
2.68-2.880.2281440.18775869X-RAY DIFFRACTION99
2.88-3.170.22261430.18315842X-RAY DIFFRACTION99
3.18-3.630.18561420.16395773X-RAY DIFFRACTION98
3.63-4.580.16231450.13795891X-RAY DIFFRACTION99
4.58-73.50.19971420.15755747X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.90290.0917-0.53170.7379-0.04811.02980.0894-0.30320.09780.06810.0145-0.00290.02750.1224-0.08220.1578-0.0408-0.00240.1694-0.02660.1061-20.521241.195833.1396
20.5095-0.0894-0.3161.006-0.07211.84790.1363-0.02610.05350.02380.07780.1253-0.5063-0.113-0.12590.1937-0.00620.06420.08520.01340.1594-34.576419.583940.4313
30.7401-0.0135-0.43670.70540.00971.15820.04130.04610.0822-0.05170.04540.1284-0.097-0.1141-0.06860.1303-0.0173-0.01010.08920.02480.1216-23.87742.214919.3236
40.93860.25150.08710.7860.23551.07720.0914-0.143-0.00820.0011-0.0582-0.01020.1068-0.1119-0.03820.0966-0.0361-0.01110.1251-0.01890.0922-36.4199-6.381327.8808
50.7002-0.11440.03240.4698-0.15921.15740.1146-0.0139-0.0375-0.07210.0972-0.1664-0.2320.4708-0.10690.0843-0.10040.01440.1789-0.08160.1947-18.18289.119736.9512
60.7415-0.0307-0.32390.73060.23831.07610.06330.09910.0899-0.092-0.0308-0.0312-0.0249-0.0089-0.01880.1054-0.0134-0.01340.0868-0.01580.082-36.7715-4.761214.0539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 132 )
2X-RAY DIFFRACTION2chain 'A' and (resid 133 through 285 )
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 417 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 133 )
5X-RAY DIFFRACTION5chain 'B' and (resid 134 through 285 )
6X-RAY DIFFRACTION6chain 'B' and (resid 286 through 416 )

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