Structure of PDB 5tma Chain B Binding Site BS01

Receptor Information
>5tma Chain B (length=561) Species: 542 (Zymomonas mobilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDYTVGTYLAERLVQIGLKHHFAVAGDYNLVLLDNLLDNKNMEQVYCCNE
LNCGFSAEGYARAKGAAAAVVTYSVGALSAFDAIGGAYAENLPVILISGA
PNNNDHAAAHVLHHALGKTDYHYQLEMAKNITAAAEAIYTPEEAPAKIDH
VIKTALREKKPVYLEIACNIASMPCAAPGPASALFNDEASDEASLNAAVE
ETLKFIENRDKVAVLVGSKLRAAAAEEAAVKFADALGGAVATMAAAKSFF
PEENPHYIGTSWGEVSYPGVEKTMKEADAVIALAPVFNDYSTTGWTDIPD
PKKLVLAEPRSVVVNGIRFPSVHLKDYLTRLAEKVSKKTGALDFFKSLNA
GELKKADPADPSAPLVNAEIARQIEDLLTPNTTVIAETGDSWFNAQRMKL
PNGARVEYEMQWGHIGWSVPAAFGYAVGAPERRNILMVGDGSFQLTAQEV
AQMVRLKLPVIIFLINNYGYTIEVMIHDGPYNNIKNWDYAALMEVFNGNS
GAGKGLKAKTAAELEEAIKVALDNTDGPTLIECFIAREDCTEELVKWGER
VAAANSRKPVN
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 chain5tma Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5tma An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme.
Resolution1.67 Å
Binding residue
(original residue number in PDB)		D390 G413 H414 I415 G439 G441 S442 N467 G469 Y470 T471 I472 E473
Binding residue
(residue number reindexed from 1)		D390 G413 H414 I415 G439 G441 S442 N467 G469 Y470 T471 I472 E473
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D27 Y28 E50 Y73 H113 H114 L116 G117 C168 Y290 T388 G413 D440 N467 G469 I472 E473
Catalytic site (residue number reindexed from 1) D27 Y28 E50 Y73 H113 H114 L116 G117 C168 Y290 T388 G413 D440 N467 G469 I472 E473
Enzyme Commision number 4.1.1.1: pyruvate decarboxylase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004737 pyruvate decarboxylase activity
GO:0016831 carboxy-lyase activity
GO:0030976 thiamine pyrophosphate binding
GO:0046872 metal ion binding
Biological Process
GO:0000949 aromatic amino acid family catabolic process to alcohol via Ehrlich pathway
GO:0019752 carboxylic acid metabolic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5tma, PDBe:5tma, PDBj:5tma
PDBsum5tma
PubMed30002729
UniProtP06672|PDC_ZYMMO Pyruvate decarboxylase (Gene Name=pdc)

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