Structure of PDB 5m1d Chain A Binding Site BS01

Receptor Information
>5m1d Chain A (length=469) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YNDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENP
KGYSMPVLCNLFGTPKRVAMGMGQEDVSALREVGKLLAFLKKQVLNMPTK
RLRGAPCQQKIVSGDDVDLNRIPIMTCWPEDAAPLITWGLTVTRGPHKER
QNLGIYRQQLIGKNKLIMRWLSHRGGALDYQEWCAAHPGERFPVSVALGA
DPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCISNDLEVPASAEIVL
EGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTG
RPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQ
YAGHAKRVMMGVWSFLRQFMYTKFVIVCDDDVNARDWNDVIWAITTRMDP
ARDTVLVENTPIDYLDFASPVSGLGSKMGLDATNKWPGETQREWGRPIKK
DPDVVAHIDAIWDELAIFN
Ligand information
Ligand IDMN
InChIInChI=1S/Mn/q+2
InChIKeyWAEMQWOKJMHJLA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mn+2]
CACTVS 3.341[Mn++]
FormulaMn
NameMANGANESE (II) ION
ChEMBL
DrugBankDB06757
ZINC
PDB chain5m1d Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5m1d Oxidative Maturation and Structural Characterization of Prenylated FMN Binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		N175 E241
Binding residue
(residue number reindexed from 1)		N152 E218
Annotation score1
Enzymatic activity
Enzyme Commision number 4.1.1.98: 4-hydroxy-3-polyprenylbenzoate decarboxylase.
Gene Ontology
Molecular Function
GO:0008694 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity
GO:0016831 carboxy-lyase activity
GO:0030145 manganese ion binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0120233 prenyl-FMNH2 binding
Biological Process
GO:0006744 ubiquinone biosynthetic process
GO:0032150 ubiquinone biosynthetic process from chorismate
GO:0034214 protein hexamerization
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5m1d, PDBe:5m1d, PDBj:5m1d
PDBsum5m1d
PubMed28057757
UniProtP0AAB4|UBID_ECOLI 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (Gene Name=ubiD)

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