5GZ4 | pdb_00005gz4

Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	GFP	e5gz4A1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: GFP	ECOD (v294.1)
A	Ald_deCOase	e5gz4A6	A: a/b three-layered sandwiches	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: Ald_deCOase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1360.180	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (utative)
A	3.40.570.10	Alpha Beta	3-Layer(aba) Sandwich	Extracellular Endonuclease	Chain A	CATH (utative)

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 nucleic acid binding toxin activity nucleoside triphosphate diphosphatase activity cation binding ion binding metal 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 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.