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BioLiP

Structure of PDB 6r2c Chain B

Receptor sequence
>6r2cB (length=815) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence]
DKNARVIELIAAYRNRGHLMADIDPLRLDNTRFWDLDREFKQRKKLRDIL
SVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYILSKL
NAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEVVIA
MPHRGRLNVLANIVGKPYSQIFSEFDVKYHLGATGTYIQMFGDNDIEVSL
TANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDNRFSVVPLMLHGDAAFA
GQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFTTAPTDSRSSEYCTDVA
KMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKKDVVIDMLCYRRRGHNE
GDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGDISMKEAEDALRDYQGQ
LERVFNEVRELEKHEIEPLATAVDKAMLQRIGDAHLALPEGFTVHPRVRP
VLEKRREMAYEGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRH
AVIVDRKTGEEFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGY
SVGNPDAMVLWEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHG
HEGQGPDHTSGRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQR
PLIVFTPKSMLRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRL
LLTSGKIYYELAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVK
EKFWVQEEPANQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSK
VHAVEQQEILDTAFG
3D structure
PDB6r2c Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: From a Michaelis-like complex to ThDP adducts.
ChainB
Resolution2.09 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 TPP B Q901 L950 E952 Q976 F980 Q489 L538 E540 Q564 F568
BS02 JQ5 B Q976 H1020 Q564 H608 MOAD: Ki=0.88mM
BS03 TPP B R540 S604 L606 G644 D645 A646 A647 N678 I680 H747 R154 S205 L207 G245 D246 A247 A248 N279 I281 H348
BS04 MG B D645 N678 I680 D246 N279 I281
BS05 CA B D1004 H1055 D1058 I1060 D592 H643 D646 I648
BS06 JQ5 B H539 S604 F682 H153 S205 F283 MOAD: Ki=0.88mM
Gene Ontology
Molecular Function
GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
GO:0030976 thiamine pyrophosphate binding

View graph for
Molecular Function
External links
PDB RCSB:6r2c, PDBe:6r2c, PDBj:6r2c
PDBsum6r2c
PubMed31476368
UniProtA0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)

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