Structure of PDB 6kdy Chain C

Receptor sequence

>6kdyC (length=335) Species: 9606 (Homo sapiens)

GVQTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWEERNVTAIQGPGGKWM
IPSEAKESMDKNKMGLKGPLKTPIAAGHPSMNLLLRKTFDLYANVRPCVS
IEGYKTPYTDVNIVTIRENTEGEYSGIEHVIVDGVVQSIKLITEGASKRI
AEFAFEYARNNHRSNVTAVHKANIMRMSDGLFLQKCREVAESCKDIKFNE
MYLDTVCLNMVQDPSQFDVLVMPNLYGDILSDLCAGLIGGLGVTPSGNIG
ANGVAIFESVHGTAPDIAGKDMANPTALLLSAVMMLRHMGLFDHAARIEA
ACFATIKDGKSLTKDLGGNAKCSDFTEEICRRVKD

3D structure

• PDB: 6kdy Molecular basis for the function of the alpha beta heterodimer of human NAD-dependent isocitrate dehydrogenase.
• Chain: C
• Resolution: 3.02 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y126 K173 D206 D230
• Catalytic site (residue number reindexed from 1): Y124 K171 D204 D228
• Enzyme Commision number: 1.1.1.41: isocitrate dehydrogenase (NAD(+)).

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	NAD	C	P71 T74 N84 H263 G264 T265 A266 D268 I269 N276	P69 T72 N82 H261 G262 T263 A264 D266 I267 N274

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0004449 isocitrate dehydrogenase (NAD+) 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:0046872 metal ion binding
• GO:0051287 NAD binding

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0006099 tricarboxylic acid cycle
• GO:0006102 isocitrate metabolic process

Cellular Component

• GO:0005634 nucleus
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix
• GO:0045242 isocitrate dehydrogenase complex (NAD+)

External links

• PDB: RCSB:6kdy, PDBe:6kdy, PDBj:6kdy
• PDBsum: 6kdy
• PubMed: 31515270
• UniProt: P50213|IDH3A_HUMAN Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (Gene Name=IDH3A)