Structure of PDB 6kma Chain D Binding Site BS05

Receptor Information
>6kma Chain D (length=836) Species: 216895 (Vibrio vulnificus CMCP6) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DAKQVKVLQLINAYRFRGHEAAELDPLGLWQRPTVAELDPAFHNLTEDDF
EETFNVGSFAVGQETMPLKDIYTALKKTYCGSIGAEYMHMTDTEQKRWIQ
QRLESVVGQPSFDKDEKRTFLAELTAAEGLERYLGAKFPGAKRFSLEGGD
AMIPMMKELIRHAGRSGMREVVIGMAHRGRLNMLVNVLGKKPQDLFDEFA
GKGTGDVKYHQGFSADFATPGGDVHLALAFNPSHLEIVNPVVMGSVRARQ
DRLGDDDGSKVLPITIHGDSAIAGQGVVAETFNMSQARGFCVGGTVRVVV
NNQVGFTTSNPRDTRSTMYCTDIAKMVQAPIFHVNADDPEAVAFVTRIAL
DYRNEFKRDVVIDLVCYRRHGHNEADEPNATQPLMYQKIKKHPTPRKLYA
DVLIDRNECDIETATQMVNEYRDALDHGEVVVKEWRPMAYLGHEWDTPWS
NTYDKQRLVELGKRLCQYPESHTLHSRVSKLYNDRTAMTNGEKELDWGMA
ETLAYATLVDDGKRIRISGQDSGRGTFFHRHAVLHNQNDASTYVPLANIH
DKQGPFEVFDSVLSEEAVLAFEYGYATAEPSGLTLWEAQFGDFANGAQVV
IDQFISSGEQKWARLCGLTMLLPHGYEGQGPEHSSARLERYLQLCAEQNM
QVVVPSTPAQVYHMIRRQVVRPMRRPLIVMSPKSLLRHPLCTSSLDDLAN
GTFMPAIPEIDELDPAKVKRVVFCSGKVYFDLLEQRRNNEQDDVAIVRIE
QLYPFPMDDVKAAIAPYVNVEDFVWCQEEPQNQGAWYCSQHNFRAAIPAG
TELKYAGRPASASPAVGYMSVHLKQQKALIDDALNV
Ligand information
Ligand IDDW3
InChIInChI=1S/C2H4O2/c3-1-2-4/h1,4H,2H2
InChIKeyWGCNASOHLSPBMP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C(C=O)O
CACTVS 3.385OCC=O
FormulaC2 H4 O2
Name2-oxidanylethanal
ChEMBLCHEMBL3884509
DrugBank
ZINCZINC000008215746
PDB chain6kma Chain D Residue 1005 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6kma 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.
Resolution2.282 Å
Binding residue
(original residue number in PDB)		H301 S324
Binding residue
(residue number reindexed from 1)		H210 S233
Annotation score1
Enzymatic activity
Enzyme Commision number 1.2.4.2: oxoglutarate dehydrogenase (succinyl-transferring).
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6kma, PDBe:6kma, PDBj:6kma
PDBsum6kma
PubMed
UniProtA0A3Q0L1E1

[Back to BioLiP]