Structure of PDB 8p5r Chain C Binding Site BS03

Receptor Information

>8p5r Chain C (length=1109) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

GDESQILRGAAAAVVKNMNASLEVPTATSVRAIPAKLMIDNRVVINNHLK
RTRGGKISFTHLLGYAIVQAVKKFPNMNRHFAVVDGKPTAITPAHTNLGL
AIDLQGKDGNRSLVVAAIKRCETMRFGQFIAAYEDIVRRARDGKLTAEDF
SGVTISLTNPGTLGTVHSVPRLMQGQGAIIGAGAMEYPAEFQGASEERIA
DLGIGKLITLTSTYDHRIIQGAESGDFLRTIHQLLLDDDFFDEIFRELGI
PYEPVRWRTDNPDSIEDKNARVIELIAAYRNRGHLMADIDPLRLDNTRFR
SHPDLDVNSHGLTLWDLDREFKVDGFAGVQRKKLRDILSVLRDAYCRHVG
VEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLNAAEAFETFLQT
KYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPHRGRLNVLAN
IVGKPYSQIFSEFEPSQAHGSGDVKYHLGATGTYIQMFGDNDIEVSLTAN
PSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFAGQG
VVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVAKMI
GAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNEGDD
PSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQLER
VFNEVRELEKHELATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRR
EMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDR
KTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPD
AMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGP
DHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFT
PKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGK
IYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQ
EEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQ
QEILDTAFG

Ligand information

• Ligand ID: TPP
• InChI: InChI=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
• InChIKey: AYEKOFBPNLCAJY-UHFFFAOYSA-O
• SMILES:
  CACTVS 3.341: Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
  OpenEye OEToolkits 1.5.0: Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
  OpenEye OEToolkits 1.5.0: Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
  CACTVS 3.341: Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
• Formula: C12 H19 N4 O7 P2 S
• Name: THIAMINE DIPHOSPHATE
• ChEMBL: CHEMBL1236376
• ZINC: ZINC000008215517
• PDB chain: 8p5r Chain C Residue 1303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p5r High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase.
• Resolution: 4.562 Å
• Binding residue (original residue number in PDB): R540 H571 S604 L606 G644 D645 A647 N678 I680 G681 H747
• Binding residue (residue number reindexed from 1): R442 H469 S502 L504 G542 D543 A545 N576 I578 G579 H645
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.2.4.2: oxoglutarate dehydrogenase (succinyl-transferring).
  2.2.1.5: 2-hydroxy-3-oxoadipate synthase.
  2.3.1.61: dihydrolipoyllysine-residue succinyltransferase.
  4.1.1.71: 2-oxoglutarate decarboxylase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0004149 dihydrolipoyllysine-residue succinyltransferase activity
• GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity
• GO:0008683 2-oxoglutarate decarboxylase activity
• 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:0016831 carboxy-lyase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding
• GO:0050439 2-hydroxy-3-oxoadipate synthase activity

Biological Process

• GO:0006099 tricarboxylic acid cycle

Cellular Component

• GO:0005829 cytosol
• GO:0045252 oxoglutarate dehydrogenase complex

External links

• PDB: RCSB:8p5r, PDBe:8p5r, PDBj:8p5r
• PDBsum: 8p5r
• PubMed: 37563123
• UniProt: A0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)