Structure of PDB 5nkk Chain D Binding Site BS01

Receptor Information
>5nkk Chain D (length=258) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKESVRFLTDFGEISDAISDLLTSSPNFNVISAIGPQGAGKSTLLSMLAG
NNSRQMYREYVFRRHQTIQIDIYIVNHQIFLDCQPMYDDSTAMSDTLRLT
AFLLYVSHTVLVVSETHYDKVIIDTLRVAEQIRPYLAIFRPKLAIDRKTN
LVFIKTKASSIDLAPTVIREREELLRLSFQDSRWLKVSQEPFKTLIVLEE
EFDEQIAELREELQKNREDFTVETAAMDEKKWLDMCREVIRDKTLHKTLK
EYQRAMTD
Ligand information
Ligand IDPOP
InChIInChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-2
InChIKeyXPPKVPWEQAFLFU-UHFFFAOYSA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
CACTVS 3.341O[P]([O-])(=O)O[P](O)([O-])=O
ACDLabs 10.04[O-]P(=O)(O)OP([O-])(=O)O
OpenEye OEToolkits 1.5.0OP(=O)([O-])OP(=O)(O)[O-]
FormulaH2 O7 P2
NamePYROPHOSPHATE 2-
ChEMBL
DrugBank
ZINC
PDB chain5nkk Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5nkk Structure of a SMG8-SMG9 complex identifies a G-domain heterodimer in the NMD effector proteins.
Resolution2.64 Å
Binding residue
(original residue number in PDB)		Q95 G98 K99 S100 T101
Binding residue
(residue number reindexed from 1)		Q37 G40 K41 S42 T43
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Biological Process
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

View graph for
Biological Process
External links
PDB RCSB:5nkk, PDBe:5nkk, PDBj:5nkk
PDBsum5nkk
PubMed28389433
UniProtQ9XWJ1|SMG9_CAEEL Nonsense-mediated mRNA decay factor SMG9 (Gene Name=smg-9)

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