Structure of PDB 6efg Chain D Binding Site BS03

Receptor Information
>6efg Chain D (length=537) Species: 284590 (Kluyveromyces lactis NRRL Y-1140) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANE
LNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGV
PSVHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDRCIRTTYVSQR
PVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVIENVLQLIKEA
KNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSIDEKHPRFGG
VYVGTLSSPAVKEAVESADLVLSVGALSYKTKNIVEFHSDYTKIRSATFP
GVQMKFALQKLLTKVADAAKGYKPVPVPSEPEHNEAVADSTPLKQEWVWT
QVGEFLREGDVVITETGTSAFGINQTHFPNNTYGISQVLWGSIGFTTGAT
LGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNND
GYTIERLIHGETAQYNCIQNWQHLELLPTFGAKDYEAVRVSTTGEWNKLT
TDEKFQDNTRIRLIEVMLPTMDAPSNLVKQAQLTAAT
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 chain6efg Chain E Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6efg The crystal structure of pyruvate decarboxylase from Kluyveromyces lactis. Implications for the substrate activation mechanism of this enzyme.
Resolution2.04 Å
Binding residue
(original residue number in PDB)		P26 E51 V76
Binding residue
(residue number reindexed from 1)		P25 E50 V75
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) L25 G27 D28 F29 N30 E51 T73 H115 L117 G118 A169 T266 T388 G413 I415 D444 N471 G473 Y474 I476 E477 I480 T542
Catalytic site (residue number reindexed from 1) L24 G26 D27 F28 N29 E50 T72 H104 L106 G107 A158 T255 T366 G391 I393 D422 N449 G451 Y452 I454 E455 I458 T520
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
Cellular Component
GO:0005634 nucleus
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:6efg, PDBe:6efg, PDBj:6efg
PDBsum6efg
PubMed
UniProtQ12629|PDC1_KLULA Pyruvate decarboxylase (Gene Name=PDC1)

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