Structure of PDB 5c0y Chain B Binding Site BS02

Receptor Information

>5c0y Chain B (length=388) Species: 559292 (Saccharomyces cerevisiae S288C)

KRVEKPQLKFKSPIDNSESHPFIPLLKEKPNALKPLSESLRLVDDDENNP
SHYPHPYEYEIDHQEYSPEILQIREEIPSKSWDDSVPIWVDTSTELESML
EDLKNTKEIAVDLEHHDYRSYYGIVCLMQISTRERDYLVDTLKLRENLHI
LNEVFTNPSIVKVFHGAFMNIIWLQRDLGLYVVGLFDTYHASKAIGLPRH
SLAYLLENFANFKTSKKYQLADWRIRPLSKPMTAYARADTHFLLNIYDQL
RNKLIESNKLAGVLYESRNVAKRRFEYSKYRPLTPSSEVYSPIKESPWKI
LMYQYNIPPEREVLVRELYQWRDLIARRDDESPRFVMPNQLLAALVAYTP
TDVIGVVSLTNGVTEHVRQNAKLLANLIRDALRNIKNT

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 5c0y Chain B Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5c0y RNA degradation paths in a 12-subunit nuclear exosome complex.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): D238 L239 E240 D365
• Binding residue (residue number reindexed from 1): D112 L113 E114 D239
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): D238 E240 N296 Y361 D365
• Catalytic site (residue number reindexed from 1): D112 E114 N170 Y235 D239
• Enzyme Commision number: 3.1.13.-

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0000175 3'-5'-RNA exonuclease activity
• GO:0003676 nucleic acid binding
• GO:0008408 3'-5' exonuclease activity

Biological Process

• GO:0000467 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006139 nucleobase-containing compound metabolic process
• GO:0044237 cellular metabolic process

External links

• PDB: RCSB:5c0y, PDBe:5c0y, PDBj:5c0y
• PDBsum: 5c0y
• PubMed: 26222026
• UniProt: Q12149|RRP6_YEAST Exosome complex exonuclease RRP6 (Gene Name=RRP6)