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Structure of PDB 5w6x Chain A

Receptor sequence
>5w6xA (length=179) Species: 9606 (Homo sapiens) [Search protein sequence]
GARRLELGEALALGSGWRHVCHALLYAPDPGMLFGRIPLRYAILMQMRFD
GRLGFPGGFVDTQDRSLEDGLNRELREELGEAAAAFRVERTDYRSSHVGS
GPRVVAHFYAKRLTLEELLAVEAGATRAKDHGLEVLGLVRVPLYTLRDGV
GGLPTFLENSFIGSAREQLLEALQDLGLL
3D structure
PDB5w6x Structural analyses of NudT16-ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins.
ChainA
Resolution2.1 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.6.1.62: 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase.
3.6.1.64: inosine diphosphate phosphatase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 APR A H24 R50 G60 F61 A108 E136 I164 S166 A167 Q170 H22 R48 G58 F59 A106 E134 I162 S164 A165 Q168
BS02 MG A E76 E80 E136 E74 E78 E134
BS03 MG A G59 E80 G57 E78
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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External links
PDB RCSB:5w6x, PDBe:5w6x, PDBj:5w6x
PDBsum5w6x
PubMed30976021
UniProtQ96DE0|NUD16_HUMAN U8 snoRNA-decapping enzyme (Gene Name=NUDT16)

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