Structure of PDB 2a8q Chain A Binding Site BS01

Receptor Information
>2a8q Chain A (length=190) Species: 8355 (Xenopus laevis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRNISREESLQLEGYKHACHALLHAPSQAKLFDRVPIRRVLLMMMRFDGR
LGFPGGFVRDISLEEGLKRELEEELGPALATVEVTEDDYRSSQVREHPQK
CVTHFYIKELKLEEIERIEAEAVNAKDHGLEVMGLIRVPLYTLRDRVGGL
PAFLCNNFIGNSKSQLLYALRSLKLLREDQIQEVLKASHR
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 chain2a8q Chain A Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2a8q Crystal structures of U8 snoRNA decapping nudix hydrolase, X29, and its metal and cap complexes
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G72 E93
Binding residue
(residue number reindexed from 1)		G55 E74
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:0035870 dITP diphosphatase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0050897 cobalt ion binding
GO:0097383 dIDP phosphatase activity
GO:0110152 RNA NAD+-cap (NAD+-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:2a8q, PDBe:2a8q, PDBj:2a8q
PDBsum2a8q
PubMed16472752
UniProtQ6TEC1|NUD16_XENLA U8 snoRNA-decapping enzyme (Gene Name=nudt16)

[Back to BioLiP]