Structure of PDB 6efh Chain A Binding Site BS01

Receptor Information

>6efh Chain A (length=557) 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
PSVSSQAKQLLLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDR
CIRTTYVSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVI
ENVLQLIKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGS
IDEKHPRFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSY
KTKNIVEFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPS
EPEHNEAVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFP
NNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTV
QEISTMIRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPT
FGAKDYEAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVK
QAQLTAA

Ligand information

Ligand ID

PY0

InChI

InChI=1S/C3H8NO3/c1-2(5)3(4,6)7/h2,5-6H,4H2,1H3/q-1/t2-,3+/m0/s1

InChIKey

ISJWJWXATCJUBY-STHAYSLISA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.6.1	CC(C(N)(O)[O-])O
CACTVS 3.352	C[CH](O)[C](N)(O)[O-]
OpenEye OEToolkits 1.6.1	C[C@@H]([C@@](N)(O)[O-])O
ACDLabs 10.04	[O-]C(O)(N)C(O)C
CACTVS 3.352	C[C@H](O)[C@@](N)(O)[O-]

Formula

C3 H8 N O3

Name

(1S,2S)-1-amino-1,2-dihydroxypropan-1-olate

ChEMBL

DrugBank

ZINC

PDB chain

6efh Chain A 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)	H92 C221 H225 G286 A287 H310 S311
Binding residue (residue number reindexed from 1)	H91 C220 H224 G285 A286 H309 S310
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 H113 H114 L116 G117 A168 T265 N292 T387 G412 I414 D443 N470 G472 Y473 I475 E476 I479 T541
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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