Structure of PDB 6b09 Chain A Binding Site BS02

Receptor Information
>6b09 Chain A (length=176) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GARRLELGEALALGWRHVCHALLYAPDPGMLFGRIPLRYAILMQMRFDGR
LGFPGGFVDTQDRSLEDGLNRELREELGEAAAAFRVERTDYRSSHVGSGP
RVVAHFYAKRLTLEELLAVEAGATRAKDHGLEVLGLVRVPLYTLRDGVGG
LPTFLENSFIGSAREQLLEALQDLGL
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain6b09 Chain A Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6b09 Structural analyses of NudT16-ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		E76 E80 E136
Binding residue
(residue number reindexed from 1)		E72 E76 E132
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.1.62: 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase.
3.6.1.64: inosine diphosphate phosphatase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0008235 metalloexopeptidase activity
GO:0016787 hydrolase activity
GO:0030145 manganese ion binding
GO:0030515 snoRNA binding
GO:0031404 chloride ion binding
GO:0035870 dITP diphosphatase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0050897 cobalt ion binding
GO:0097383 dIDP phosphatase activity
GO:0110153 RNA NAD-cap (NMN-forming) hydrolase activity
GO:0140933 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
GO:1990003 IDP phosphatase activity
GO:1990174 phosphodiesterase decapping endonuclease activity
Biological Process
GO:0006402 mRNA catabolic process
GO:0009117 nucleotide metabolic process
GO:0016077 sno(s)RNA catabolic process
GO:0035863 dITP catabolic process
GO:0090068 positive regulation of cell cycle process
GO:0110155 NAD-cap decapping
GO:2000233 negative regulation of rRNA processing
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm

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Molecular Function
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Cellular Component
External links
PDB RCSB:6b09, PDBe:6b09, PDBj:6b09
PDBsum6b09
PubMed30976021
UniProtQ96DE0|NUD16_HUMAN U8 snoRNA-decapping enzyme (Gene Name=NUDT16)

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