Structure of PDB 2vk4 Chain B Binding Site BS03

Receptor Information

>2vk4 Chain B (length=557) Species: 28985 (Kluyveromyces lactis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANE
LNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGV
PSVSSQALLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDRCIR
TTYVSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVIENV
LQLIKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSIDE
KHPRFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSYKTK
NIVEFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPSEPE
HNEAVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFPNNT
YGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEI
STMIRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPTFGA
KDYEAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVKQAQ
LTAATNA

Ligand information

Ligand ID

InChI

InChI=1S/Mg/q+2

InChIKey

JLVVSXFLKOJNIY-UHFFFAOYSA-N

SMILES

Software	SMILES
ACDLabs 10.04 OpenEye OEToolkits 1.5.0	[Mg+2]
CACTVS 3.341	[Mg++]

Formula

Name

MAGNESIUM ION

PDB chain

2vk4 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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Structure summary

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PDB	2vk4 The Crystal Structure of Pyruvate Decarboxylase from Kluyveromyces Lactis. Implications for the Substrate Activation Mechanism of This Enzyme.
Resolution	1.95 Å
Binding residue (original residue number in PDB)	D444 N471 G473
Binding residue (residue number reindexed from 1)	D440 N467 G469
Annotation score	1

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 E477 I480 T542
Catalytic site (residue number reindexed from 1)	L24 G26 D27 F28 N29 E50 T72 H110 H111 L113 G114 A165 T262 N289 T384 G409 I411 D440 N467 G469 Y470 I472 E473 I476 T538
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:2vk4, PDBe:2vk4, PDBj:2vk4
PDBsum	2vk4
PubMed
UniProt	Q12629\|PDC1_KLULA Pyruvate decarboxylase (Gene Name=PDC1)

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