Structure of PDB 5yvt Chain A

Receptor sequence
>5yvtA (length=332) Species: 9606 (Homo sapiens) [Search protein sequence]
VQTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWEERNVTAIQGPGGKWMI
PSEAKESMDKNKMGLKGPLKTPIAAPSMNLLLRKTFDLYANVRPCVSIEG
YKTPYTDVNIVTIRENTEGEYSGIEHVIVDGVVQSIKLITEGASKRIAEF
AFEYARNNHRSNVTAVHKANIMRMSDGLFLQKCREVAESCKDIKFNEMYL
DTVCLNMVQDPSQFDVLVMPNLYGDILSDLCAGLIGGLGVTPSGNIGANG
VAIFESVHGTAPDIAGKDMANPTALLLSAVMMLRHMGLFDHAARIEAACF
ATIKDGKSLTKDLGGNAKCSDFTEEICRRVKD
3D structure
PDB5yvt Insights into the inhibitory mechanisms of NADH on the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase.
ChainA
Resolution2.4 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) Y126 K173 D206 D230 D234
Catalytic site (residue number reindexed from 1) Y121 K168 D201 D225 D229
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 MG A D230 D234 D225 D229
BS02 NAI A L72 T74 N84 E260 V262 H263 G264 I269 N276 D317 L69 T71 N79 E255 V257 H258 G259 I264 N271 D312 MOAD: Kd=109uM
PDBbind-CN: -logKd/Ki=3.96,Kd=109uM
BS03 NAI A N175 D206 N170 D201 MOAD: Kd=109uM
PDBbind-CN: -logKd/Ki=3.96,Kd=109uM
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+)

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5yvt, PDBe:5yvt, PDBj:5yvt
PDBsum5yvt
PubMed29453450
UniProtP50213|IDH3A_HUMAN Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial (Gene Name=IDH3A)

[Back to BioLiP]