6G4G | pdb_00006g4g

Full length ectodomain of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3) including the SMB domains but with a partially disordered active site structure

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	Phosphodiest_C	e6g4gD5	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)
D	Phosphodiest_N	e6g4gD4	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)
D	Endonuclease_NS	e6g4gD2	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)
D	Somatomedin_B	e6g4gD1	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)
C	Phosphodiest_C	e6g4gC4	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)
C	Phosphodiest_N	e6g4gC1	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)
C	Endonuclease_NS	e6g4gC5	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)
C	Somatomedin_B	e6g4gC2	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)
B	Phosphodiest_C	e6g4gB5	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)
B	Phosphodiest_N	e6g4gB2	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)
B	Endonuclease_NS	e6g4gB4	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)
B	Somatomedin_B	e6g4gB1	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)
A	Phosphodiest_C	e6g4gA2	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	e6g4gA1	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	e6g4gA5	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	e6g4gA4	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.720.10	Alpha Beta	3-Layer(aba) Sandwich	Alkaline Phosphatase, subunit A	Alkaline Phosphatase, subunit A	CATH (utative)
D	3.30.1360.180	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (utative)
D	3.40.570.10	Alpha Beta	3-Layer(aba) Sandwich	Extracellular Endonuclease	Chain A	CATH (utative)
C	3.40.720.10	Alpha Beta	3-Layer(aba) Sandwich	Alkaline Phosphatase, subunit A	Alkaline Phosphatase, subunit A	CATH (utative)
C	3.30.1360.180	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (utative)
C	3.40.570.10	Alpha Beta	3-Layer(aba) Sandwich	Extracellular Endonuclease	Chain A	CATH (utative)
B	3.40.720.10	Alpha Beta	3-Layer(aba) Sandwich	Alkaline Phosphatase, subunit A	Alkaline Phosphatase, subunit A	CATH (utative)
B	3.30.1360.180	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (utative)
B	3.40.570.10	Alpha Beta	3-Layer(aba) Sandwich	Extracellular Endonuclease	Chain A	CATH (utative)
A	3.40.720.10	Alpha Beta	3-Layer(aba) Sandwich	Alkaline Phosphatase, subunit A	Alkaline Phosphatase, subunit A	CATH (utative)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01033	Somatomedin B domain (Somatomedin_B)	Somatomedin B domain	-	Family
A, B, C, D	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, B, C, D	Ectonucleotide pyrophosphatase/phosphodiesterase family member 3	pyrophosphatase activity bis(5'-adenosyl)-triphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding nucleic acid binding nucleoside triphosphate diphosphatase activity pyrophosphatase activity bis(5'-adenosyl)-triphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding nucleic acid binding nucleoside triphosphate diphosphatase activity GTP diphosphatase activity bis(5'-adenosyl)-pentaphosphatase activity phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds nuclease activity phosphodiesterase I activity phosphoric diester hydrolase activity catalytic activity, acting on a nucleic acid exonuclease activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding ATP diphosphatase activity UTP diphosphatase activity dinucleotide phosphatase activity bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity bis(5'-nucleosyl)-tetraphosphatase activity transition metal ion binding zinc ion binding	nucleoside phosphate metabolic process ribose phosphate metabolic process purine nucleoside triphosphate metabolic process ATP metabolic process carbohydrate derivative metabolic process primary metabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process nucleoside phosphate metabolic process ribose phosphate metabolic process purine nucleoside triphosphate metabolic process ATP metabolic process carbohydrate derivative metabolic process primary metabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process phosphorus metabolic process regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus biological regulation negative regulation of biological process response to external stimulus regulation of inflammatory response regulation of response to stimulus response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response developmental process smooth muscle cell differentiation regulation of cellular process regulation of developmental process cellular developmental process regulation of smooth muscle cell differentiation regulation of cell differentiation muscle cell differentiation muscle structure development regulation of muscle cell differentiation cell differentiation anatomical structure development phosphate ion homeostasis inorganic ion homeostasis chemical homeostasis homeostatic process basophil activation involved in immune response multicellular organismal process immune response cell activation cell activation involved in immune response myeloid leukocyte activation myeloid cell activation involved in immune response leukocyte activation immune effector process basophil activation immune system process leukocyte activation involved in immune response granulocyte activation regulation of immune effector process regulation of leukocyte activation positive regulation of biological process regulation of cell activation regulation of mast cell activation involved in immune response negative regulation of cellular process mast cell activation regulation of immune system process regulation of mast cell activation regulation of multicellular organismal process positive regulation of immune effector process positive regulation of immune system process negative regulation of immune response negative regulation of immune effector process negative regulation of cell activation negative regulation of mast cell activation mast cell activation involved in immune response negative regulation of immune system process negative regulation of mast cell activation involved in immune response regulation of immune response negative regulation of multicellular organismal process negative regulation of leukocyte activation regulation of leukocyte proliferation negative regulation of cell population proliferation cell population proliferation leukocyte proliferation negative regulation of leukocyte proliferation regulation of mast cell proliferation regulation of cell population proliferation negative regulation of mast cell proliferation mast cell proliferation pyrimidine-containing compound metabolic process pyrimidine nucleotide metabolic process catabolic process nucleoside triphosphate catabolic process organophosphate catabolic process nucleoside phosphate catabolic process nucleobase-containing compound catabolic process	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane apical part of cell plasma membrane region apical plasma membrane extracellular region intracellular anatomical structure perinuclear region of cytoplasm cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

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

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.