Structure of PDB 8p5x Chain D Binding Site BS03

Receptor Information
>8p5x Chain D (length=1082) Species: 196627 (Corynebacterium glutamicum ATCC 13032) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PGQTPIRGIFKSIAKNMDISLEIPTATSVRDMPARLMFENRAMVNDQLKR
TRGGKISFTHIIGYAMVKAVMAHPDMNNSYDVIDGKPTLIVPEHINLGLA
IDLPQKDGSRALVVAAIKETEKMNFSEFLAAYEDIVARSRKGKLTMDDYQ
GVTVSLTNPGGIGTRHSVPRLTKGQGTIIGVGSMDYPAEFQGASEDRLAE
LGVGKLVTITSTYDHRVIQGAVSGEFLRTMSRLLTDDSFWDEIFDAMNVP
YTPMRWAQDVPNTGVDKNTRVMQLIEAYRSRGHLIADTNPLSWVQPGMPV
PDHRDLDIETHNLTIWDLDRTFNVGGFGGKETMTLREVLSRLRAAYTLKV
GSEYTHILDRDERTWLQDRLEAGMPKPTQAEQKYILQKLNAAEAFENFLQ
TKYVGQKRFSLEGAEALIPLMDSAIDTAAGQGLDEVVIGMPHRGRLNVLF
NIVGKPLASIFNGDVKYHLGSEGQHLQMFGDGEIKVSLTANPSHLEAVNP
VMEGIVRAKQDYLDKGVDGKTVVPLLLHGDAAFAGLGIVPETINLAKLRG
YDVGGTIHIVVNNQIGFTTTPDSSRSMHYATDYAKAFGCPVFHVNGDDPE
AVVWVGQLATEYRRRFGKDVFIDLVCYRLRGHNEADDPSMTQPKMYELIT
GRETVRAQYTEDLLGRGDLSNEDAEAVVRDFHDQMESVFNGLETNISREE
LLELGQAFANTPEGFNYHPRVAPVAKKRVSSVTEGGIDWAWGELLAFGSL
ANSGRLVRLAGEDSRRGTFTQRHAVAIDPATAEEFNPLHELAQSKGNNGK
FLVYNSALTEYAGMGFEYGYSVGNEDSIVAWEAQFGDFANGAQTIIDEYV
SSGEAKWGQTSKLILLLPHGYEGQGPDHSSARIERFLQLCAEGSMTVAQP
STPANHFHLLRRHALSDLKRPLVIFTPKSMLRNKAAASAPEDFTEVTKFQ
SVINDPNVADAAKVKKVMLVSGKLYYELAKRKEKDGRDDIAIVRIEMLHP
IPFNRISEALAGYPNAEEVLFVQDEPANQGPWPFYQEHLPELIPNMPKMR
RVSRRAQSSTATGVAKVHQLEEKQLIDEAFEA
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 chain8p5x Chain D Residue 1302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8p5x High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase.
Resolution2.29 Å
Binding residue
(original residue number in PDB)		D645 N678 I680
Binding residue
(residue number reindexed from 1)		D530 N563 I565
Annotation score1
Enzymatic activity
Enzyme Commision number 1.2.4.2: oxoglutarate dehydrogenase (succinyl-transferring).
2.3.1.61: dihydrolipoyllysine-residue succinyltransferase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004149 dihydrolipoyllysine-residue succinyltransferase activity
GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
GO:0016746 acyltransferase activity
GO:0030976 thiamine pyrophosphate binding
GO:0046872 metal ion binding
Biological Process
GO:0006099 tricarboxylic acid cycle
Cellular Component
GO:0005829 cytosol
GO:0045252 oxoglutarate dehydrogenase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8p5x, PDBe:8p5x, PDBj:8p5x
PDBsum8p5x
PubMed37563123
UniProtQ8NRC3|ODO12_CORGL 2-oxoglutarate dehydrogenase E1/E2 component (Gene Name=odhA)

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