Structure of PDB 6syt Chain C Binding Site BS02

Receptor Information

>6syt Chain C (length=309) Species: 9606 (Homo sapiens)

LLPPERMKHSIKLVDDQMNWCDSAIEYLLDQTDVLVVGVLGLQGTGKSMV
MSLLSANTPEEDQRTYVFRAQSAEMKERGGNQTSGIDFFITQERIVFLDT
QPILSPSILDHLINNYNLPHTYVEMQSLQIAAFLFTVCHVVIVVQDWFTD
LSLYRFLQTAEMVKPSTEYYPHLVFLQNKARREDFCPRKLRQMHLMIDQL
MAHSHLRYKGTLSMLQCNVFPGLPPDFLDSEVNLFLVPFMDPLFSLLPGY
RGHPSFQSLVSKLRSQVMSMARPQLSHTILTEKNWFHYAARIWDGVRKSS
ALAEYSRLL

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: 6syt Chain C Residue 602

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6syt InsP6binding to PIKK kinases revealed by the cryo-EM structure of an SMG1-SMG8-SMG9 complex.
• Resolution: 3.45 Å
• Binding residue (original residue number in PDB): S218 T253
• Binding residue (residue number reindexed from 1): S48 T83
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0042802 identical protein binding

Biological Process

• GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
• GO:0001654 eye development
• GO:0001701 in utero embryonic development
• GO:0007420 brain development
• GO:0007507 heart development
• GO:0043066 negative regulation of apoptotic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:6syt, PDBe:6syt, PDBj:6syt
• PDBsum: 6syt
• PubMed: 31792449
• UniProt: Q9H0W8|SMG9_HUMAN Nonsense-mediated mRNA decay factor SMG9 (Gene Name=SMG9)