Structure of PDB 6b09 Chain A

Receptor sequence
>6b09A (length=176) Species: 9606 (Homo sapiens) [Search protein sequence]
GARRLELGEALALGWRHVCHALLYAPDPGMLFGRIPLRYAILMQMRFDGR
LGFPGGFVDTQDRSLEDGLNRELREELGEAAAAFRVERTDYRSSHVGSGP
RVVAHFYAKRLTLEELLAVEAGATRAKDHGLEVLGLVRVPLYTLRDGVGG
LPTFLENSFIGSAREQLLEALQDLGL
3D structure
PDB6b09 Structural analyses of NudT16-ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins.
ChainA
Resolution3.2 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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 C7G A R20 H24 R50 G60 F61 E76 E136 I164 S166 Q170 R16 H20 R46 G56 F57 E72 E132 I160 S162 Q166
BS02 MG A E76 E80 E136 E72 E76 E132
BS03 C7G A R149 D150 R145 D146
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

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

[Back to BioLiP]