Structure of PDB 6x7u Chain A Binding Site BS02

Receptor Information
>6x7u Chain A (length=162) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WRHACHALLYAPDPGMLFGRIPLRYAILMQMRFDGRLGFPGGFVDTQDRS
LEDGLNRELREELGEAAAAFRVERTDYRSSHVGSGPRVVAHFYAKRLTLE
ELLAVEAGATRAKDHGLEVLGLVRVPLYTLRDGVGGLPTFLENSFIGSAR
EQLLEALQDLGL
Ligand information
Ligand IDMN
InChIInChI=1S/Mn/q+2
InChIKeyWAEMQWOKJMHJLA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mn+2]
CACTVS 3.341[Mn++]
FormulaMn
NameMANGANESE (II) ION
ChEMBL
DrugBankDB06757
ZINC
PDB chain6x7u Chain A Residue 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6x7u Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		G59 E80
Binding residue
(residue number reindexed from 1)		G41 E62
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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Biological Process
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Cellular Component
External links
PDB RCSB:6x7u, PDBe:6x7u, PDBj:6x7u
PDBsum6x7u
PubMed32432673
UniProtQ96DE0|NUD16_HUMAN U8 snoRNA-decapping enzyme (Gene Name=NUDT16)

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