Structure of PDB 6r2b Chain C

Receptor sequence

>6r2bC (length=844) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

DKNARVIELIAAYRNRGHLMADIDPLRLDNTRGLTLWDLDREFKVRKKLR
DILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKYIL
SKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLDEV
VIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHGSGDVKYHLGAT
GTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGSDN
RFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIGFT
TAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAFKK
DVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGRGD
ISMKEAEDALRDYQGQLERVFNEVRELEKHEIEPSESVEADQQIPSKLAT
AVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFAEL
LALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLATN
PDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFVNG
AQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQLWA
EGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSDIR
DFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKENRE
DVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFGLT
LPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG

3D structure

• PDB: 6r2b 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.
• Chain: C
• Resolution: 1.96 Å

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	QSP	C	H539 R540 Y578 H579 S604 H605 L606 G644 D645 A646 A647 N678 I680 G681 H747	H156 R157 Y195 H196 S221 H222 L223 G261 D262 A263 A264 N295 I297 G298 H364
BS02	MG	C	D645 N678 I680	D262 N295 I297
BS03	CA	C	D1004 H1055 D1058 I1060	D621 H672 D675 I677
BS04	QSP	C	Q901 L950 E952 Q976 F980 H1020	Q518 L567 E569 Q593 F597 H637

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

External links

• PDB: RCSB:6r2b, PDBe:6r2b, PDBj:6r2b
• PDBsum: 6r2b
• PubMed: 31476368
• UniProt: A0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)