Structure of PDB 8bay Chain A

Receptor sequence

>8bayA (length=414) Species: 9606 (Homo sapiens) [Search protein sequence]

KKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDAT
NDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNI
LGGTVFREAIICKNIPRLVSGWVKPIIIGCHAYGDQYRATDFVVPGPGKV
EITYTPSDGTQKVTYLVHNFEEGGGVAMGMYNQDKSIEDFAHSSFQMALS
KGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLID
DMVAQAMKSEGGFIWACKNYDGDVQSDFVAQGYGSLGMMTSVLVCPDGKT
VEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKEL
AFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLG
ENLKIKLAQAKLLE

3D structure

PDB

8bay Natural and synthetic 2-oxoglutarate derivatives are substrates for oncogenic variants of human isocitrate dehydrogenase 1 and 2.

Chain

Resolution

2.35 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)
BS01	NDP	A	T75 I76 T77 R82 A308 H309 G310 T311 V312 R314 H315 T327 N328	T73 I74 T75 R80 A306 H307 G308 T309 V310 R312 H313 T325 N326
BS02	QDC	A	T77 S94 N96 G97 R109 Y139 D275	T75 S92 N94 G95 R107 Y137 D273
BS03	QD8	A	T77 S94 N96 R109 Y139 D275	T75 S92 N94 R107 Y137 D273
BS04	CA	A	D275 D279	D273 D277

Gene Ontology

	Molecular Function
GO:0000287	magnesium ion binding
GO:0004450	isocitrate dehydrogenase (NADP+) activity
GO:0005515	protein binding
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:0045296	cadherin binding
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:0006739	NADP 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:0005576	extracellular region
GO:0005737	cytoplasm
GO:0005739	mitochondrion
GO:0005777	peroxisome
GO:0005782	peroxisomal matrix
GO:0005829	cytosol
GO:0034774	secretory granule lumen
GO:0070062	extracellular exosome
GO:1904724	tertiary granule lumen
GO:1904813	ficolin-1-rich granule lumen

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:8bay, PDBe:8bay, PDBj:8bay
PDBsum	8bay
PubMed	36621625
UniProt	O75874\|IDHC_HUMAN Isocitrate dehydrogenase [NADP] cytoplasmic (Gene Name=IDH1)

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