Structure of PDB 8p5x Chain B Binding Site BS01

Receptor Information
>8p5x Chain B (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 IDTPP
InChIInChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
InChIKeyAYEKOFBPNLCAJY-UHFFFAOYSA-O
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
FormulaC12 H19 N4 O7 P2 S
NameTHIAMINE DIPHOSPHATE
ChEMBLCHEMBL1236376
DrugBank
ZINCZINC000008215517
PDB chain8p5x Chain A Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		E901 L947 E949 Q973 F977
Binding residue
(residue number reindexed from 1)		E762 L808 E810 Q834 F838
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

View graph for
Molecular Function
View graph for
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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