Structure of PDB 1pyd Chain A Binding Site BS01

Receptor Information
>1pyd Chain A (length=537) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRWAGNANE
LNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGV
PSISHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVT
QRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILALVK
DAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGSISEQHPRY
GGVYVGTLSKPEVKEAVESADLILSVGALLSDKTKNIVEFHSDHMKIRNA
TFPGVQMKFVLQKLLTNIADAAKGYKPVAVPARTPANAAVPASTPLKQEW
MWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTT
GATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVL
NNDGYTIEKLIHGPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWD
KLTQDKSFNDNSKIRMIEIMLPVFDAPQNLVKQAKLT
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain1pyd Chain A Residue 559 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1pyd Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at 2.4-A resolution.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D444 N471 G473
Binding residue
(residue number reindexed from 1)		D425 N452 G454
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) L25 G27 D28 F29 N30 E51 T73 H114 H115 L117 G118 A169 T266 T388 G413 I415 D444 N471 G473 Y474 I476 E477 I480 V542
Catalytic site (residue number reindexed from 1) L24 G26 D27 F28 N29 E50 T72 H105 H106 L108 G109 A160 T257 T369 G394 I396 D425 N452 G454 Y455 I457 E458 I461 V523
Enzyme Commision number 4.1.1.-
4.1.1.43: phenylpyruvate decarboxylase.
4.1.1.72: branched-chain-2-oxoacid decarboxylase.
4.1.1.74: indolepyruvate decarboxylase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004737 pyruvate decarboxylase activity
GO:0005515 protein binding
GO:0016831 carboxy-lyase activity
GO:0030976 thiamine pyrophosphate binding
GO:0046872 metal ion binding
GO:0047433 branched-chain-2-oxoacid decarboxylase activity
GO:0047434 indolepyruvate decarboxylase activity
GO:0050177 phenylpyruvate decarboxylase activity
Biological Process
GO:0000949 aromatic amino acid family catabolic process to alcohol via Ehrlich pathway
GO:0000955 amino acid catabolic process via Ehrlich pathway
GO:0006090 pyruvate metabolic process
GO:0006559 L-phenylalanine catabolic process
GO:0006569 tryptophan catabolic process
GO:0009083 branched-chain amino acid catabolic process
GO:0019655 glycolytic fermentation to ethanol
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol

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Cellular Component
External links
PDB RCSB:1pyd, PDBe:1pyd, PDBj:1pyd
PDBsum1pyd
PubMed8512926
UniProtP06169|PDC1_YEAST Pyruvate decarboxylase isozyme 1 (Gene Name=PDC1)

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