Structure of PDB 8k5p Chain O Binding Site BS01

Receptor Information
>8k5p Chain O (length=346) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKEIGFYSRTKDEEYLISDDTNLNYYYLPDAELDRKLDLSSGFQKFKDYY
KDFEDRCSLRGLLETIESSERHKGKKINADIITFRGIARKLISCAFDSPS
FNTVDLRIVSFNGQLFIKEQDLNVFTGYKFETLATLSNPLQYTPREVIEK
RTKRIVSHGDEYISVVRTGVGNCKLILGAEVDCIFDFKENGRDNLKHYAE
LKCTQQVANISDTHKFERKLFRTWLQCFLVGIPRIIYGFKDDHYVLKTVE
EFSTEEVPVLLKNNNPQVGSACLEAIKWYGLLTEWLLKMIPRDEDPHSQI
RAFKLVFENNHLRLSEIEESDEEYSGLIDGEHILSNGFKEWRKSLK
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 chain8k5p Chain O Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8k5p Structural basis of exoribonuclease-mediated mRNA transcription termination
Resolution2.8 Å
Binding residue
(original residue number in PDB)		D223 E241
Binding residue
(residue number reindexed from 1)		D182 E200
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:0030234 enzyme regulator activity
GO:0034353 mRNA 5'-diphosphatase activity
GO:0046872 metal ion binding
GO:0110152 RNA NAD+-cap (NAD+-forming) 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:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000956 nuclear-transcribed mRNA catabolic process
GO:0006353 DNA-templated transcription termination
GO:0006364 rRNA processing
GO:0006397 mRNA processing
GO:0030846 termination of RNA polymerase II transcription, poly(A)-coupled
GO:0031087 deadenylation-independent decapping of nuclear-transcribed mRNA
GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process
GO:0110155 NAD-cap decapping
GO:1904595 positive regulation of termination of RNA polymerase II transcription
Cellular Component
GO:0005634 nucleus
GO:0005829 cytosol
GO:0090730 Las1 complex
GO:0110103 RNA polymerase II termination complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8k5p, PDBe:8k5p, PDBj:8k5p
PDBsum8k5p
PubMed38538796
UniProtP53063|DXO_YEAST Decapping nuclease RAI1 (Gene Name=RAI1)

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