Structure of PDB 5z9x Chain A Binding Site BS02

Receptor Information

>5z9x Chain A (length=288) Species: 3702 (Arabidopsis thaliana)

ELKLATAEKQVLDELVKLLQSRDLRGENGNWKEFLHVYDKNADSPSDPSR
RSHEDLVQFLTTFKKKEDLQLLKCHANHLLIENLKQESQDEDTPEQMLVR
LTVEHPSYSLDYSFKPYSEDWFVSDVGMKMKKVMESTNMVAVDCEMVLCE
DGTEGLVRVGVVDRDLKVILDEFVKPNKPVVDYRTDITGITAEDIENASL
SVVDIQETLQPFLSTGTILVGHSLNRDLEVLKIDHPKVIDTALVFKLRRP
SLNNLCKSILGYGVPHDCVHDASAAMKLALAVVEKRVD

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: 5z9x Chain A Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5z9x Structural and biochemical insights into small RNA 3' end trimming by Arabidopsis SDN1.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): D144 C280 D283
• Binding residue (residue number reindexed from 1): D143 C268 D271
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.1.-.-

Gene Ontology

Molecular Function

• GO:0000175 3'-5'-RNA exonuclease activity
• GO:0003676 nucleic acid binding
• GO:0004527 exonuclease activity
• GO:0005515 protein binding
• GO:0008408 3'-5' exonuclease activity
• GO:0035198 miRNA binding
• GO:0044748 3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing

Biological Process

• GO:0010587 miRNA catabolic process
• GO:0044747 pre-miRNA 3'-end processing

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:5z9x, PDBe:5z9x, PDBj:5z9x
• PDBsum: 5z9x
• PubMed: 30181559
• UniProt: A3KPE8|SDN1_ARATH Small RNA degrading nuclease 1 (Gene Name=SDN1)