Structure of PDB 8p5r Chain C

Receptor sequence
>8p5rC (length=1109) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence]
GDESQILRGAAAAVVKNMNASLEVPTATSVRAIPAKLMIDNRVVINNHLK
RTRGGKISFTHLLGYAIVQAVKKFPNMNRHFAVVDGKPTAITPAHTNLGL
AIDLQGKDGNRSLVVAAIKRCETMRFGQFIAAYEDIVRRARDGKLTAEDF
SGVTISLTNPGTLGTVHSVPRLMQGQGAIIGAGAMEYPAEFQGASEERIA
DLGIGKLITLTSTYDHRIIQGAESGDFLRTIHQLLLDDDFFDEIFRELGI
PYEPVRWRTDNPDSIEDKNARVIELIAAYRNRGHLMADIDPLRLDNTRFR
SHPDLDVNSHGLTLWDLDREFKVDGFAGVQRKKLRDILSVLRDAYCRHVG
VEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKLNAAEAFETFLQT
KYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIAMPHRGRLNVLAN
IVGKPYSQIFSEFEPSQAHGSGDVKYHLGATGTYIQMFGDNDIEVSLTAN
PSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFAGQG
VVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVAKMI
GAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNEGDD
PSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQLER
VFNEVRELEKHELATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRR
EMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDR
KTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPD
AMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGP
DHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFT
PKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGK
IYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQ
EEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQ
QEILDTAFG
3D structure
PDB8p5r High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase.
ChainC
Resolution4.562 Å
3D
structure
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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.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 MG C G644 D645 N678 G542 D543 N576
BS02 CA C D1004 G1056 G1059 D886 G938 G941
BS03 TPP C R540 H571 S604 L606 G644 D645 A647 N678 I680 G681 H747 R442 H469 S502 L504 G542 D543 A545 N576 I578 G579 H645
BS04 TPP C L950 E952 F980 L832 E834 F862
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8p5r, PDBe:8p5r, PDBj:8p5r
PDBsum8p5r
PubMed37563123
UniProtA0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)

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