Structure of PDB 6kma Chain D Binding Site BS04

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 IDTPP
InChIInChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
InChIKeyAYEKOFBPNLCAJY-UHFFFAOYSA-O
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
FormulaC12 H19 N4 O7 P2 S
NameTHIAMINE DIPHOSPHATE
ChEMBLCHEMBL1236376
DrugBank
ZINCZINC000008215517
PDB chain6kma Chain D Residue 1004 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		H263 R264 S324 L326 G359 D360 S361 A362 Q366 N393 V395 G396 H463
Binding residue
(residue number reindexed from 1)		H177 R178 S233 L235 G268 D269 S270 A271 Q275 N302 V304 G305 H372
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

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

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