Structure of PDB 5yzh Chain B

Receptor sequence
>5yzhB (length=409) Species: 10090 (Mus musculus) [Search protein sequence]
KIQGGSVVEMQGDEMTRIIWELIKEKLILPYVELDLHSYDLGIENRDATN
DQVTKDAAEAIKKYNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNIL
GGTVFREAIICKNIPRLVTGWVKPIIIGRHAYGDQYRATDFVVPGPGKVE
ITYTPKDGTQKVTYMVHDFEEGGGVAMGMYNQDKSIEDFAHSSFQMALSK
GWPLYLSTKNTILKKYDGRFKDIFQEIYDKKYKSQFEAQKICYEHRLIDD
MVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLICPDGKTV
EAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWSRGLAHRAKLDNNTELS
FFAKALEDVCIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGE
NLKAKLAQA
3D structure
PDB5yzh NADP+-dependent cytosolic isocitrate dehydrogenase provides NADPH in the presence of cadmium due to the moderate chelating effect of glutathione.
ChainB
Resolution1.994 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 1.1.1.42: isocitrate dehydrogenase (NADP(+)).
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 NAP B D253 Q257 K260 D250 Q254 K257
BS02 NAP B T75 T77 N96 L288 H309 G310 T311 V312 T313 R314 H315 N328 T72 T74 N93 L285 H306 G307 T308 V309 T310 R311 H312 N325
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004450 isocitrate dehydrogenase (NADP+) activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0050661 NADP binding
GO:0051287 NAD binding
Biological Process
GO:0006097 glyoxylate cycle
GO:0006099 tricarboxylic acid cycle
GO:0006102 isocitrate metabolic process
GO:0006103 2-oxoglutarate metabolic process
GO:0006749 glutathione metabolic process
GO:0006979 response to oxidative stress
GO:0008585 female gonad development
GO:0014070 response to organic cyclic compound
GO:0048545 response to steroid hormone
GO:0060696 regulation of phospholipid catabolic process
GO:0071071 regulation of phospholipid biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005777 peroxisome
GO:0005829 cytosol

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5yzh, PDBe:5yzh, PDBj:5yzh
PDBsum5yzh
PubMed29923039
UniProtO88844|IDHC_MOUSE Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=Idh1)

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