Structure of PDB 6wug Chain A Binding Site BS01

Receptor Information
>6wug Chain A (length=312) Species: 4896 (Schizosaccharomyces pombe) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLREFSFYDVPPAHVPPVSEPLEIACYSLSRDRELLLDDSKLSYYYPPPL
FSDLNTGFPNRFHPPKSDPDPISIVKDVLMTKGIQMNSSFLTWRGLITKI
MCAPLDPRNHWETYLVMDPTSGIIMMEERTNQDRMCYWGYKFEAISTLPE
IWDAQDVVPDEQYCSIVKINIGKSKLILAGEVDCIWDKKPENPNLHYVEL
KTSKKYPLENYGMRKKLLKYWAQSFLLGIGRIIIGFRDDNGILIEMKELF
THQIPKMLRPYFKPNDWTPNRLLVVLEHALEWIKQTVKQHPPSTEFTLSY
TGGSKLVLRQII
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain6wug Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6wug DXO/Rai1 enzymes remove 5'-end FAD and dephospho-CoA caps on RNAs.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		E150 D201 E239 L240
Binding residue
(residue number reindexed from 1)		E143 D183 E199 L200
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.1.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0004518 nuclease activity
GO:0005515 protein binding
GO:0019003 GDP binding
GO:0034353 mRNA 5'-diphosphatase activity
GO:0046872 metal ion binding
GO:0110152 RNA NAD+-cap (NAD+-forming) hydrolase activity
GO:0140432 5'-hydroxyl dinucleotide hydrolase activity
GO:1990174 phosphodiesterase decapping endonuclease activity
Biological Process
GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000956 nuclear-transcribed mRNA catabolic process
GO:0006397 mRNA processing
GO:0110155 NAD-cap decapping
Cellular Component
GO:0005634 nucleus
GO:0005829 cytosol
GO:0090730 Las1 complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6wug, PDBe:6wug, PDBj:6wug
PDBsum6wug
PubMed32374864
UniProtO13836|DXO_SCHPO Decapping nuclease din1 (Gene Name=din1)

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