Structure of PDB 5yvt Chain B

Receptor sequence
>5yvtB (length=333) Species: 9606 (Homo sapiens) [Search protein sequence]
RHTVTMIPGDGIGPELMLHVKSVFRHACVPVDFEEVHVSSNADEEDIRNA
IMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLDLYANVIHCKSLPG
VVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEY
AFKLAQESGRKKVTAVHKANIMKLGDGLFLQCCREVAARYPQITFENMIV
DNTTMQLVSRPQQFDVMVMPNLYGNIVNNVCAGLVGGPGLVAGANYGHVY
AVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATSIRKAVL
ASMDNENMHTPDIGGQGTTSEAIQDVIRHIRVI
3D structure
PDB5yvt Insights into the inhibitory mechanisms of NADH on the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase.
ChainB
Resolution2.4 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) Y135 K182 D215 N239 N243
Catalytic site (residue number reindexed from 1) Y121 K168 D201 N225 N229
Enzyme Commision number ?
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 NAI B I26 E80 T81 P252 G253 R272 N273 T274 G275 S277 I278 A284 N285 D326 I12 E66 T67 P238 G239 R258 N259 T260 G261 S263 I264 A270 N271 D312 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:0005524 ATP binding
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:0005730 nucleolus
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:5yvt, PDBe:5yvt, PDBj:5yvt
PDBsum5yvt
PubMed29453450
UniProtP51553|IDH3G_HUMAN Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial (Gene Name=IDH3G)

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