5GZ5

Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra) in complex with AMP

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Phosphodiest_C	e5gz5A3	A: a+b two layers	X: Alpha-beta plaits	H: Phosphonoacetate hydrolase insertion domain (From Topology)	T: Phosphonoacetate hydrolase insertion domain	F: Phosphodiest_C	ECOD (1.6)
A	Phosphodiest_N	e5gz5A4	A: a/b three-layered sandwiches	X: Alkaline phosphatase-like (From Topology)	H: Alkaline phosphatase-like (From Topology)	T: Alkaline phosphatase-like	F: Phosphodiest_N	ECOD (1.6)
A	Endonuclease_NS	e5gz5A1	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: Endonuclease_NS	ECOD (1.6)
A	Somatomedin_B	e5gz5A2	A: few secondary structure elements	X: Somatomedin B domain (From Topology)	H: Somatomedin B domain (From Topology)	T: Somatomedin B domain	F: Somatomedin_B	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01033	Somatomedin B domain (Somatomedin_B)	Somatomedin B domain	-	Family
A	PF01223	DNA/RNA non-specific endonuclease (Endonuclease_NS)	DNA/RNA non-specific endonuclease	-	Domain
A	PF01663	Type I phosphodiesterase / nucleotide pyrophosphatase (Phosphodiest)	Type I phosphodiesterase / nucleotide pyrophosphatase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Snake venom phosphodiesterase (PDE)	pyrophosphatase activity nucleoside diphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity ADP phosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity binding organic cyclic compound binding nucleic acid binding toxin activity nucleoside triphosphate diphosphatase activity cation binding ion binding pyrophosphatase activity nucleoside diphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity ADP phosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity binding organic cyclic compound binding nucleic acid binding toxin activity nucleoside triphosphate diphosphatase activity cation binding ion binding metal ion binding small molecule binding	nucleoside phosphate metabolic process catabolic process nucleoside triphosphate catabolic process organophosphate catabolic process primary metabolic process nucleoside phosphate catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process nucleoside phosphate metabolic process catabolic process nucleoside triphosphate catabolic process organophosphate catabolic process primary metabolic process nucleoside phosphate catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process nucleoside triphosphate metabolic process phosphorus metabolic process	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002591	Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase	Family
A	IPR044929	DNA/RNA non-specific endonuclease superfamily	Homologous Superfamily
A	IPR044925	His-Me finger superfamily	Homologous Superfamily
A	IPR036024	Somatomedin B-like domain superfamily	Homologous Superfamily
A	IPR001604	DNA/RNA non-specific endonuclease/pyrophosphatase/phosphodiesterase domain	Domain
A	IPR020821	ENPP1-3/EXOG-like, endonuclease/phosphodiesterase domain	Domain
A	IPR001212	Somatomedin B domain	Domain
A	IPR017850	Alkaline-phosphatase-like, core domain superfamily	Homologous Superfamily

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.