Structure of PDB 6kdy Chain A

Receptor sequence
>6kdyA (length=335) Species: 9606 (Homo sapiens) [Search protein sequence]
GVQTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWEERNVTAIQGPGGKWM
IPSEAKESMDKNKMGLKGPLKTPIAAGHPSMNLLLRKTFDLYANVRPCVS
IEGYKTPYTDVNIVTIRENTEGEYSGIEHVIVDGVVQSIKLITEGASKRI
AEFAFEYARNNHRSNVTAVHKANIMRMSDGLFLQKCREVAESCKDIKFNE
MYLDTVCLNMVQDPSQFDVLVMPNLYGDILSDLCAGLIGGLGVTPSGNIG
ANGVAIFESVHGTAPDIAGKDMANPTALLLSAVMMLRHMGLFDHAARIEA
ACFATIKDGKSLTKDLGGNAKCSDFTEEICRRVKD
3D structure
PDB6kdy Molecular basis for the function of the alpha beta heterodimer of human NAD-dependent isocitrate dehydrogenase.
ChainA
Resolution3.02 Å
3D
structure
Catalytic site residues are labeled in the structure
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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 A P71 L72 T74 N84 H263 G264 T265 A266 D268 I269 N276 D317 P69 L70 T72 N82 H261 G262 T263 A264 D266 I267 N274 D315
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+)

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Molecular Function
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Cellular Component
External links
PDB RCSB:6kdy, PDBe:6kdy, PDBj:6kdy
PDBsum6kdy
PubMed31515270
UniProtP50213|IDH3A_HUMAN Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (Gene Name=IDH3A)

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