Structure of PDB 6efh Chain B Binding Site BS03

Receptor Information

>6efh Chain B (length=556) Species: 284590 (Kluyveromyces lactis NRRL Y-1140) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANE
LNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGV
PSVSSLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDRCIRTTY
VSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVIENVLQL
IKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGSIDEKHP
RFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSYKTKNIV
EFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPSEPEHNE
AVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFPNNTYGI
SQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTM
IRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPTFGAKDY
EAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVKQAQLTA
ATNAKN

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

6efh 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	6efh Covalently bound substrate at the regulatory site of yeast pyruvate decarboxylases triggers allosteric enzyme activation.
Resolution	2.99 Å
Binding residue (original residue number in PDB)	T390 I415 G443 S446 N471 G473 Y474 T475 I476 E477
Binding residue (residue number reindexed from 1)	T383 I408 G436 S439 N464 G466 Y467 T468 I469 E470
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 H107 H108 L110 G111 A162 T259 N286 T381 G406 I408 D437 N464 G466 Y467 I469 E470 I473 T535
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:6efh, PDBe:6efh, PDBj:6efh
PDBsum	6efh
PubMed
UniProt	Q12629\|PDC1_KLULA Pyruvate decarboxylase (Gene Name=PDC1)

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