5GRH

Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+)

> Summary

Summary for 5GRH

Related5GRI 5GRL 5GRF 5GRE
DescriptorIsocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (E.C.1.1.1.41), Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial (E.C.1.1.1.41)
Functional Keywordsapo-form, isocitrate dehydrogenase, oxidoreductase
Biological sourceHomo sapiens (Human)
Cellular locationMitochondrion P50213 P51553
Total number of polymer chains2
Total molecular weight75574
Authors
Ma, T.,Peng, Y. (deposition date: 2016-08-11, release date: 2017-02-15)
Primary citation
Ma, T.,Peng, Y.,Huang, W.,Ding, J.
Molecular mechanism of the allosteric regulation of the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase.
Sci Rep, 7:40921-40921, 2017
PubMed: 28098230
DOI: 10.1038/srep40921
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.8 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.256803.6%2.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5grh
no rotation
Molmil generated image of 5grh
rotated about x axis by 90°
Molmil generated image of 5grh
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AIsocitrate dehydrogenase [NAD] subunit alpha, mitochondrialpolymer33936682.21
UniProt (P50213)
Pfam (PF00180)
Homo sapiens (Human)Isocitric dehydrogenase subunit alpha,NAD(+)-specific ICDH subunit alpha
BIsocitrate dehydrogenase [NAD] subunit gamma, mitochondrialpolymer35438867.51
UniProt (P51553)
Pfam (PF00180)
Homo sapiens (Human)Isocitric dehydrogenase subunit gamma,NAD(+)-specific ICDH subunit gamma
MAGNESIUM IONnon-polymer24.31

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight75549.7
Non-Polymers*Number of molecules1
Total molecular weight24.3
All*Total molecular weight75574.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.8 Å)

Cell axes118.397118.397143.163
Cell angles90.0090.00120.00
SpacegroupP 31 2 1
Resolution limits19.71 - 2.80
the highest resolution shell value2.873 - 2.800
R-factor0.2257
R-work0.22390
the highest resolution shell value0.362
R-free0.25920
the highest resolution shell value0.416
RMSD bond length0.006
RMSD bond angle1.088

Data Collection Statistics

Resolution limits19.71 - 2.80
the highest resolution shell value -
Number of reflections28718
Completeness98.9
Redundancy10.8

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC13binding site for residue MG A 401
ChainResidue
AASP230
AASP234
BASP215

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI24Substrate. {ECO:0000250}.
ChainResidueDetails
AARG88
AARG98
AARG119
AASP206

SWS_FT_FI53Substrate. {ECO:0000250}.
ChainResidueDetails
BARG97
BARG128
BASP215

SWS_FT_FI71NAD. {ECO:0000255}.
ChainResidueDetails
BTHR17-VAL45

SWS_FT_FI81ATP. {ECO:0000255}.
ChainResidueDetails
BALA270-SER277

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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