6SCX | pdb_00006scx

Crystal structure of the catalytic domain of human NUDT12 in complex with 7-methyl-guanosine-5'-triphosphate

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	NUDIX_1	e6scxC1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
C	UNK_F_TYPE	e6scxC3	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: UNK_F_TYPE	ECOD (1.6)
C	RNA_POL_M_15KD_like	e6scxC2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: RNA_POL_M_15KD_like	ECOD (1.6)
B	NUDIX_1	e6scxB3	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
B	UNK_F_TYPE	e6scxB1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: UNK_F_TYPE	ECOD (1.6)
B	RNA_POL_M_15KD_like	e6scxB2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: RNA_POL_M_15KD_like	ECOD (1.6)
A	NUDIX_1	e6scxA2	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_1	ECOD (1.6)
A	UNK_F_TYPE	e6scxA1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: UNK_F_TYPE	ECOD (1.6)
A	RNA_POL_M_15KD_like	e6scxA3	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: RNA_POL_M_15KD_like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.90.79.20	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase		CATH (utative)
C	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (utative)
B	3.90.79.20	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase		CATH (utative)
B	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (utative)
A	3.90.79.20	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase		CATH (utative)
A	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF09296	NADH pyrophosphatase-like rudimentary NUDIX domain (NUDIX-like)	NADH pyrophosphatase-like rudimentary NUDIX domain	The N-terminal domain in NADH pyrophosphatase, which has a rudiment Nudix fold according to SCOP.	Domain
A, B, C	PF09297	NADH pyrophosphatase zinc ribbon domain (Zn_ribbon_NUD)	NADH pyrophosphatase zinc ribbon domain	This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure.	Domain
A, B, C	PF00293	NUDIX domain (NUDIX)	NUDIX domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Peroxisomal NADH pyrophosphatase NUDT12	pyrophosphatase activity NADPH pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity dinucleotide phosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity NAD+ diphosphatase activity NADH pyrophosphatase activity cation binding magnesium ion binding ion binding binding metal ion binding pyrophosphatase activity NADPH pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity dinucleotide phosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity NAD+ diphosphatase activity NADH pyrophosphatase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding phosphodiesterase decapping endonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity RNA NAD-cap (NMN-forming) hydrolase activity transition metal ion binding zinc ion binding	NAD-cap decapping nucleobase-containing compound metabolic process RNA metabolic process metabolic process cellular process primary metabolic process macromolecule metabolic process nucleic acid metabolic process RNA decapping pyridine nucleotide catabolic process catabolic process organophosphate catabolic process nucleoside phosphate catabolic process purine nucleotide metabolic process NAD-cap decapping nucleobase-containing compound metabolic process RNA metabolic process metabolic process cellular process primary metabolic process macromolecule metabolic process nucleic acid metabolic process RNA decapping pyridine nucleotide catabolic process catabolic process organophosphate catabolic process nucleoside phosphate catabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process NAD+ catabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleotide catabolic process NAD+ metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process purine nucleotide catabolic process purine-containing compound catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process organophosphate metabolic process pyridine-containing compound catabolic process regulation of biosynthetic process rhythmic process regulation of biological process regulation of cellular process circadian regulation of gene expression circadian rhythm biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of biological process macromolecule catabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process mRNA catabolic process negative regulation of metabolic process mRNA metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process mRNA methylguanosine-cap decapping NADP+ metabolic process NADP+ catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle peroxisome microbody intracellular membrane-bounded organelle peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen organelle lumen microbody lumen cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle peroxisome microbody intracellular membrane-bounded organelle peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen organelle lumen microbody lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, B, C	IPR015375	NADH pyrophosphatase-like, N-terminal	Domain
A, B, C	IPR015376	Zinc ribbon, NADH pyrophosphatase	Domain
A, B, C	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B, C	IPR002110	Ankyrin repeat	Repeat
A, B, C	IPR049734	NADH pyrophosphatase-like, C-terminal domain	Domain
A, B, C	IPR050241	NAD-capped RNA hydrolase NudC subfamily	Family
A, B, C	IPR000086	NUDIX hydrolase domain	Domain
A, B, C	IPR020084	NUDIX hydrolase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: Q9BQG2	interstitial cystitis pancreatic ductal adenocarcinoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm ovarian cancer ulcerative colitis

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.