Structure of PDB 5ulj Chain B Binding Site BS01

Receptor Information

>5ulj Chain B (length=386) Species: 322104 (Scheffersomyces stipitis CBS 6054)

LVPRGSHMMKTLSLQSRAKKQPKEIFAFARDIDGEFVYDQKIVKDENVSY
YYLPDSKIDGSIDLQAGYAKFKKIPEEKNMSDMKCLLTALTKYEQEHNNG
EKVNVDIITYRGLMTKLLALPYNLNDPVDLNVLAYDGQLFINSDEEIELA
RRKEEDEHKQQSMTPEKYDHMKRCEFSGYKFEAIATLPKPWAKKMVNNYE
QYISVIKTGIGEAKMLLAGEVDCVWDYIPEDGKDVLSHYMELKTTRILES
NGQVVNFEKKLFKTWAQCFLMGIRKVVYGFRDDSFFLRDVELYKTEEIPL
LIKNNALTENKSGGKINCTTALKWYGAVIEWLLQEIPRDDTSKAYRVSFD
PSTRTFTLRELMGNENSRLRNGEMLTSEFKQWRESI

Ligand information

• Ligand ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 5ulj Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ulj 5' End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes RNA Decay through DXO-Mediated deNADding.
• Resolution: 1.911 Å
• Binding residue (original residue number in PDB): D230 E249 L250
• Binding residue (residue number reindexed from 1): D222 E241 L242
• Annotation score: 1

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:0034353 mRNA 5'-diphosphatase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0000956 nuclear-transcribed mRNA catabolic process
• GO:0006397 mRNA processing
• GO:0110155 NAD-cap decapping

Cellular Component

• GO:0005634 nucleus
• GO:0005829 cytosol

External links

• PDB: RCSB:5ulj, PDBe:5ulj, PDBj:5ulj
• PDBsum: 5ulj
• PubMed: 28283058
• UniProt: A3LNL5|DXO_PICST Decapping nuclease RAI1 (Gene Name=RAI1)