Structure of PDB 6kma Chain B Binding Site BS01

Receptor Information
>6kma Chain B (length=837) 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
GKWGTGDVKYHQGFSADFATPGGDVHLALAFNPSHLEIVNPVVMGSVRAR
QDRLGDDDGSKVLPITIHGDSAIAGQGVVAETFNMSQARGFCVGGTVRVV
VNNQVGFTTSNPRDTRSTMYCTDIAKMVQAPIFHVNADDPEAVAFVTRIA
LDYRNEFKRDVVIDLVCYRRHGHNEADEPNATQPLMYQKIKKHPTPRKLY
ADVLIDRNECDIETATQMVNEYRDALDHGEVVVKEWRPMAYLGHEWDTPW
SNTYDKQRLVELGKRLCQYPESHTLHSRVSKLYNDRTAMTNGEKELDWGM
AETLAYATLVDDGKRIRISGQDSGRGTFFHRHAVLHNQNDASTYVPLANI
HDKQGPFEVFDSVLSEEAVLAFEYGYATAEPSGLTLWEAQFGDFANGAQV
VIDQFISSGEQKWARLCGLTMLLPHGYEGQGPEHSSARLERYLQLCAEQN
MQVVVPSTPAQVYHMIRRQVVRPMRRPLIVMSPKSLLRHPLCTSSLDDLA
NGTFMPAIPEIDELDPAKVKRVVFCSGKVYFDLLEQRRNNEQDDVAIVRI
EQLYPFPMDDVKAAIAPYVNVEDFVWCQEEPQNQGAWYCSQHNFRAAIPA
GTELKYAGRPASASPAVGYMSVHLKQQKALIDDALNV
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 A 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)		Q619 L662 E664 Q688 F692
Binding residue
(residue number reindexed from 1)		Q521 L564 E566 Q590 F594
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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