Structure of PDB 8p5v Chain F Binding Site BS04

Receptor Information

>8p5v Chain F (length=1121) Species: 196627 (Corynebacterium glutamicum ATCC 13032)

PEPGQTPIRGIFKSIAKNMDISLEIPTATSVRDMPARLMFENRAMVNDQL
KRTRGGKISFTHIIGYAMVKAVMAHPDMNNSYDVIDGKPTLIVPEHINLG
LAIDLPQKDGSRALVVAAIKETEKMNFSEFLAAYEDIVARSRKGKLTMDD
YQGVTVSLTNPGGIGTRHSVPRLTKGQGTIIGVGSMDYPAEFQGASEDRL
AELGVGKLVTITSTYDHRVIQGAVSGEFLRTMSRLLTDDSFWDEIFDAMN
VPYTPMRWAQDVPNTGVDKNTRVMQLIEAYRSRGHLIADTNPLSWVQPGM
PVPDHRDLDIETHNLTIWDLDRTFNVGGFGGKETMTLREVLSRLRAAYTL
KVGSEYTHILDRDERTWLQDRLEAGMPKPTQAEQKYILQKLNAAEAFENF
LQTKYVGQKRFSLEGAEALIPLMDSAIDTAAGQGLDEVVIGMPHRGRLNV
LFNIVGKPLASIFNEFEGQMEQGQIGGSGDVKYHLGSEGQHLQMFGDGEI
KVSLTANPSHLEAVNPVMEGIVRAKQDYLDKGVDGKTVVPLLLHGDAAFA
GLGIVPETINLAKLRGYDVGGTIHIVVNNQIGFTTTPDSSRSMHYATDYA
KAFGCPVFHVNGDDPEAVVWVGQLATEYRRRFGKDVFIDLVCYRLRGHNE
ADDPSMTQPKMYELITGRETVRAQYTEDLLGRGDLSNEDAEAVVRDFHDQ
MESVFNEVKEGGKKQAEAQTGITGSQKLPHGLETNISREELLELGQAFAN
TPEGFNYHPRVAPVAKKRVSSVTEGGIDWAWGELLAFGSLANSGRLVRLA
GEDSRRGTFTQRHAVAIDPATAEEFNPLHELAQSKGNNGKFLVYNSALTE
YAGMGFEYGYSVGNEDSIVAWEAQFGDFANGAQTIIDEYVSSGEAKWGQT
SKLILLLPHGYEGQGPDHSSARIERFLQLCAEGSMTVAQPSTPANHFHLL
RRHALSDLKRPLVIFTPKSMLRNKAAASAPEDFTEVTKFQSVINDPNVAD
AAKVKKVMLVSGKLYYELAKRKEKDGRDDIAIVRIEMLHPIPFNRISEAL
AGYPNAEEVLFVQDEPANQGPWPFYQEHLPELIPNMPKMRRVSRRAQSST
ATGVAKVHQLEEKQLIDEAFE

Ligand information

• Ligand ID: ACO
• InChI: InChI=1S/C23H38N7O17P3S/c1-12(31)51-7-6-25-14(32)4-5-26-21(35)18(34)23(2,3)9-44-50(41,42)47-49(39,40)43-8-13-17(46-48(36,37)38)16(33)22(45-13)30-11-29-15-19(24)27-10-28-20(15)30/h10-11,13,16-18,22,33-34H,4-9H2,1-3H3,(H,25,32)(H,26,35)(H,39,40)(H,41,42)(H2,24,27,28)(H2,36,37,38)/t13-,16-,17-,18+,22-/m1/s1
• InChIKey: ZSLZBFCDCINBPY-ZSJPKINUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  CACTVS 3.341: CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
  ACDLabs 10.04: O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)C
  CACTVS 3.341: CC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: CC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
• Formula: C23 H38 N7 O17 P3 S
• Name: ACETYL COENZYME *A
• ChEMBL: CHEMBL1230809
• ZINC: ZINC000008551095
• PDB chain: 8p5v Chain F Residue 1302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p5v High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase.
• Resolution: 2.07 Å
• Binding residue (original residue number in PDB): P828 H829 G830 G1032 M1034 T1035 R1051 L1057 K1087 S1090 M1136 P1139 I1140 P1141 F1142 N1143 R1144
• Binding residue (residue number reindexed from 1): P729 H730 G731 G933 M935 T936 R952 L958 K988 S991 M1037 P1040 I1041 P1042 F1043 N1044 R1045
• Annotation score: 3

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

External links

• PDB: RCSB:8p5v, PDBe:8p5v, PDBj:8p5v
• PDBsum: 8p5v
• PubMed: 37563123
• UniProt: Q8NRC3|ODO12_CORGL 2-oxoglutarate dehydrogenase E1/E2 component (Gene Name=odhA)