Structure of PDB 6kma Chain D

Receptor sequence

>6kmaD (length=836) Species: 216895 (Vibrio vulnificus CMCP6)

DAKQVKVLQLINAYRFRGHEAAELDPLGLWQRPTVAELDPAFHNLTEDDF
EETFNVGSFAVGQETMPLKDIYTALKKTYCGSIGAEYMHMTDTEQKRWIQ
QRLESVVGQPSFDKDEKRTFLAELTAAEGLERYLGAKFPGAKRFSLEGGD
AMIPMMKELIRHAGRSGMREVVIGMAHRGRLNMLVNVLGKKPQDLFDEFA
GKGTGDVKYHQGFSADFATPGGDVHLALAFNPSHLEIVNPVVMGSVRARQ
DRLGDDDGSKVLPITIHGDSAIAGQGVVAETFNMSQARGFCVGGTVRVVV
NNQVGFTTSNPRDTRSTMYCTDIAKMVQAPIFHVNADDPEAVAFVTRIAL
DYRNEFKRDVVIDLVCYRRHGHNEADEPNATQPLMYQKIKKHPTPRKLYA
DVLIDRNECDIETATQMVNEYRDALDHGEVVVKEWRPMAYLGHEWDTPWS
NTYDKQRLVELGKRLCQYPESHTLHSRVSKLYNDRTAMTNGEKELDWGMA
ETLAYATLVDDGKRIRISGQDSGRGTFFHRHAVLHNQNDASTYVPLANIH
DKQGPFEVFDSVLSEEAVLAFEYGYATAEPSGLTLWEAQFGDFANGAQVV
IDQFISSGEQKWARLCGLTMLLPHGYEGQGPEHSSARLERYLQLCAEQNM
QVVVPSTPAQVYHMIRRQVVRPMRRPLIVMSPKSLLRHPLCTSSLDDLAN
GTFMPAIPEIDELDPAKVKRVVFCSGKVYFDLLEQRRNNEQDDVAIVRIE
QLYPFPMDDVKAAIAPYVNVEDFVWCQEEPQNQGAWYCSQHNFRAAIPAG
TELKYAGRPASASPAVGYMSVHLKQQKALIDDALNV

3D structure

• PDB: 6kma Understanding the molecular properties of the E1 subunit (SucA) of alpha-ketoglutarate dehydrogenase complex from Vibrio vulnificus for the enantioselective ligation of acetaldehydes into (R)-acetoin.
• Chain: D
• Resolution: 2.282 Å

Enzymatic activity

• Enzyme Commision number: 1.2.4.2: oxoglutarate dehydrogenase (succinyl-transferring).

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	D	Q619 L662 E664 Q688 F692	Q520 L563 E565 Q589 F593
BS02	DW3	D	F689 F692 H732	F590 F593 H633
BS03	MG	D	D360 N393 V395	D269 N302 V304
BS04	TPP	D	H263 R264 S324 L326 G359 D360 S361 A362 Q366 N393 V395 G396 H463	H177 R178 S233 L235 G268 D269 S270 A271 Q275 N302 V304 G305 H372
BS05	DW3	D	H301 S324	H210 S233

Gene Ontology

Molecular Function

• GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity
• GO:0016491 oxidoreductase activity
• GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
• 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:6kma, PDBe:6kma, PDBj:6kma
• PDBsum: 6kma
• UniProt: A0A3Q0L1E1