Structure of PDB 5grf Chain B Binding Site BS02

Receptor Information
>5grf Chain B (length=335) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RHTVTMIPGDGIGPELMLHVKSVFRHACVPVDFEEVHVSSNADEEDIRNA
IMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLDLYANVIHCKSLPG
VVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLAIITKAKSLRIAEY
AFKLAQESGRKKVTAVHKANIMKLGDGLFLQCCREVAARYPQITFENMIV
DNTTMQLVSRPQQFDVMVMPNLYGNIVNNVCAGLVGGPGLVAGANYGHVY
AVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATSIRKAVL
ASMDNENMHTPDIGGQGTTSEAIQDVIRHIRVING
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain5grf Chain B Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5grf Molecular mechanism of the allosteric regulation of the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		N78 R272
Binding residue
(residue number reindexed from 1)		N64 R258
Annotation score1
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 1.1.1.41: isocitrate dehydrogenase (NAD(+)).
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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Biological Process
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Cellular Component
External links
PDB RCSB:5grf, PDBe:5grf, PDBj:5grf
PDBsum5grf
PubMed28098230
UniProtP51553|IDH3G_HUMAN Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial (Gene Name=IDH3G)

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