Structure of PDB 3eya Chain D Binding Site BS02

Receptor Information
>3eya Chain D (length=520) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KQTVAAYIAKTLESAGVKRIWGVTGDSLNGLSDSLNRMGTIEWMSTRHEE
VAAFAAGAEAQLSGELAVCAGSCGPGNLHLINGLFDCHRNHVPVLAIAAH
IPSSEIGSGYFQETHPQELFRECSHYCELVSSPEQIPQVLAIAMRKAVLN
RGVSVVVLPGDVALKPAPEGATMHWYHAPQPVVTPEEEELRKLAQLLRYS
SNIALMCGSGCAGAHKELVEFAGKIKAPIVHALRGKEHVEYDNPYDVGMT
GLIGFSSGFHTMMNADTLVLLGTQFPYRAFYPTDAKIIQIDINPASIGAH
SKVDMALVGDIKSTLRALLPLVEEKADRKFLDKALEDYRDARKGLDDLAK
PSEKAIHPQYLAQQISHFAADDAIFTCDVGTPTVWAARYLKMNGKRRLLG
SFNHGSMANAMPQALGAQATEPERQVVAMCGDGGFSMLMGDFLSVVQMKL
PVKIVVFNNSVLGFVGTELHDTNFARIAEACGITGIRVEKASEVDEALQR
AFSIDGPVLVDVVVAKEELA
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 chain3eya Chain D Residue 611 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3eya Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		G381 T382 M408 G432 D433 G434 G435 N460 V462 L463 G464 F465 V466
Binding residue
(residue number reindexed from 1)		G380 T381 M407 G431 D432 G433 G434 N459 V461 L462 G463 F464 V465
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) V24 G26 D27 S28 L29 E50 S73 F112 Q113 G161 L253 A280 V380 G406 M408 D433 N460 V462 L463 F465 V466 K529
Catalytic site (residue number reindexed from 1) V23 G25 D26 S27 L28 E49 S72 F111 Q112 G160 L252 A279 V379 G405 M407 D432 N459 V461 L462 F464 V465 K516
Enzyme Commision number 1.2.5.1: pyruvate dehydrogenase (quinone).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0008289 lipid binding
GO:0016491 oxidoreductase activity
GO:0030976 thiamine pyrophosphate binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0048039 ubiquinone binding
GO:0050660 flavin adenine dinucleotide binding
GO:0052737 pyruvate dehydrogenase (quinone) activity
Biological Process
GO:0006090 pyruvate metabolic process
GO:0019752 carboxylic acid metabolic process
GO:0042867 pyruvate catabolic process
Cellular Component
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3eya, PDBe:3eya, PDBj:3eya
PDBsum3eya
PubMed18988747
UniProtP07003|POXB_ECOLI Pyruvate dehydrogenase [ubiquinone] (Gene Name=poxB)

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