Structure of PDB 2vk4 Chain A Binding Site BS01

Receptor Information

>2vk4 Chain A (length=560) Species: 28985 (Kluyveromyces lactis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANE
LNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGV
PSVQAKQLLLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDRCI
RTTYVSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVIEN
VLQLIKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSID
EKHPRFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSYKT
KNIVEFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPSEP
EHNEAVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFPNN
TYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQE
ISTMIRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPTFG
AKDYEAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVKQA
QLTAATNAKN

Ligand information

Ligand ID

TPP

InChI

InChI=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

InChIKey

AYEKOFBPNLCAJY-UHFFFAOYSA-O

SMILES

Software	SMILES
CACTVS 3.341	Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0	Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0	Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341	Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N

Formula

C12 H19 N4 O7 P2 S

Name

THIAMINE DIPHOSPHATE

PDB chain

2vk4 Chain A Residue 600 [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)	T390 G413 I415 G443 G445 S446 N471 G473 Y474 T475 I476 E477
Binding residue (residue number reindexed from 1)	T387 G410 I412 G440 G442 S443 N468 G470 Y471 T472 I473 E474
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 H111 H112 L114 G115 A166 T263 N290 T385 G410 I412 D441 N468 G470 Y471 I473 E474 I477 T539
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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