Structure of PDB 2vk4 Chain C Binding Site BS01

Receptor Information

>2vk4 Chain C (length=555) Species: 28985 (Kluyveromyces lactis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANE
LNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGV
PSAKQLLLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDRCIRT
TYVSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVIENVL
QLIKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSIDEK
HPRFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSYKTKN
IVEFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPSEPEH
NEAVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFPNNTY
GISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEIS
TMIRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPTFGAK
DYEAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVKQAQL
TAATN

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 C 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 S414 I415 G443 G445 S446 N471 G473 Y474 T475 I476 E477
Binding residue (residue number reindexed from 1)	T385 G408 S409 I410 G438 G440 S441 N466 G468 Y469 T470 I471 E472
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 H109 H110 L112 G113 A164 T261 N288 T383 G408 I410 D439 N466 G468 Y469 I471 E472 I475 T537
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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