Structure of PDB 8wd8 Chain B Binding Site BS06

Receptor Information

>8wd8 Chain B (length=750) Species: 277988 (Thermococcus thioreducens)

MLMKVLTNMVKLNQDIIPNEIYLYKIFNKPEDGMNIYKIAYRNHGIVIDP
QNRIIATPSELEYSGKFAIEDEISFNELPENYQNRLVLRILRDNGISDHA
LSRTLQKYRKPKPFGDFEVIPEIRSSVIKHGGDFYLVLHLSHQIRSKKTL
WELVGRNKDALRDFLKEHRGTILLRDIASEHKVVYKPIFKRYNGDPDLIE
DNSNDVEHWYDYHLERYWNTPELKKEFYKKFGPVDLNQPIILAKPLRQHN
RGDLVHLLPQFVVPVYNAEQLNDILASEILEYLKLTSNQRISLLSRLIND
IKTNTNIIVSSLTELEANTFDVDLNDMLQVRNADNVKVTLSELEISKTRL
FTWMKSRKYPVILPYDIPQKLKKIEKIPVFIIVDSALSRDIQTFAKDEFR
YLISSLQKSLSNWVDFPILDIRDKYIFTIDLTSDKDIVNLSIKLVNLMKN
AELGLALIATRTKLPNETFDEVKKRLFSVNIISQVVNEATLYKRDKYNES
RLNLYVQHNLLFQILSKLGIKYYVLRHKFSYDYIVGIDVTPMKLSHGYIG
GSAVMFDSQGYIRKIIPVEIGEQMGESIDMKEFFKDMVVQFGKFGIDLEG
KSILILRDGKITKDEEEGLAYISKVFGIKITTFNIVKRHLLRIFANRKLY
LRLANSVYLLPHRIKQSVGTPVPLKLSEKRLILDGTITSQEITYNDIFEI
LLLSELNYGSISADMKLPAPVHYAHKFVRALRKGWRIREELLAEGFLYFV

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: 8wd8 Chain B Residue 803

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8wd8 Molecular mechanism for target recognition, dimerization, and activation of Pyrococcus furiosus Argonaute.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): D538 D608
• Binding residue (residue number reindexed from 1): D538 D608
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding

External links

• PDB: RCSB:8wd8, PDBe:8wd8, PDBj:8wd8
• PDBsum: 8wd8
• PubMed: 38295801
• UniProt: A0A0Q2M2Z1