Structure of PDB 2vk8 Chain B Binding Site BS03

Receptor Information
>2vk8 Chain B (length=562) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRWAGNANE
LNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGV
PSISAQAKQLLLHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDR
CIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVI
DTILVLDKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGS
IDEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSDFNTGSFSYSY
KTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTTIADAAKGYKPVAVPA
RTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFP
NNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTV
QEISTMIRWGLKPYLFVLNNDGYTIQKLIHGPKAQYNEIQGWDHLSLLPT
FGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEVMLPVFDAPQNLVE
QAKLTAATNAKQ
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 chain2vk8 Chain B Residue 1565 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vk8 Covalently Bound Substrate at the Regulatory Site of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation.
Resolution1.42 Å
Binding residue
(original residue number in PDB)		D444 N471 G473
Binding residue
(residue number reindexed from 1)		D443 N470 G472
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) L25 G27 D28 F29 N30 E51 T73 H114 H115 L117 G118 A169 T266 N293 T388 G413 I415 D444 N471 G473 Y474 I476 Q477 I480 V542
Catalytic site (residue number reindexed from 1) L24 G26 D27 F28 N29 E50 T72 H113 H114 L116 G117 A168 T265 N292 T387 G412 I414 D443 N470 G472 Y473 I475 Q476 I479 V541
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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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2vk8, PDBe:2vk8, PDBj:2vk8
PDBsum2vk8
PubMed19246454
UniProtP06169|PDC1_YEAST Pyruvate decarboxylase isozyme 1 (Gene Name=PDC1)

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