1D3V

CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH 2(S)-AMINO-6-BORONOHEXANOIC ACID, AN L-ARGININE ANALOG

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1d3va_	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	Arginase-like amidino hydrolases	Arginase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1d3vb_	Alpha and beta proteins (a/b)	Arginase/deacetylase	Arginase/deacetylase	Arginase-like amidino hydrolases	Arginase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Arginase-like amidino hydrolases	8031955	4000424	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Arginase/deacetylase-like	8044333	3000260	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Arginase/deacetylase-like	8044333	3000260	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Arginase	e1d3vA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Arginase	ECOD (1.6)
B	Arginase	e1d3vB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Arginase/deacetylase	F: Arginase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.800.10	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.3.0)
B	3.40.800.10	Alpha Beta	3-Layer(aba) Sandwich	Arginase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00491	Arginase family (Arginase)	Arginase family	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PROTEIN (ARGINASE)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds arginase activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	response to stimulus response to chemical response to xenobiotic stimulus response to stress response to wounding response to axon injury immune response immune system process adaptive immune response response to methylmercury developmental process multicellular organismal process mammary gland morphogenesis mammary gland development response to stimulus response to chemical response to xenobiotic stimulus response to stress response to wounding response to axon injury immune response immune system process adaptive immune response response to methylmercury developmental process multicellular organismal process mammary gland morphogenesis mammary gland development gland development animal organ development anatomical structure morphogenesis gland morphogenesis tissue remodeling anatomical structure development mammary gland involution animal organ morphogenesis response to interleukin-4 response to peptide response to cytokine cellular response to cytokine stimulus cellular response to interleukin-4 neutrophil-mediated killing of symbiont cell regulation of immune effector process regulation of myeloid leukocyte mediated immunity positive regulation of response to biotic stimulus positive regulation of leukocyte mediated immunity regulation of cellular process neutrophil-mediated killing of fungus regulation of neutrophil mediated killing of fungus disruption of cell in another organism regulation of killing of cells of another organism regulation of programmed cell death response to biotic stimulus myeloid leukocyte mediated immunity positive regulation of neutrophil mediated cytotoxicity positive regulation of leukocyte mediated cytotoxicity positive regulation of neutrophil mediated killing of symbiont cell leukocyte mediated immunity regulation of immune system process biological process involved in interaction with symbiont positive regulation of immune system process killing of cells of another organism regulation of biological process positive regulation of programmed cell death response to other organism response to external stimulus leukocyte mediated cytotoxicity cell death immune effector process regulation of leukocyte mediated immunity regulation of defense response to fungus regulation of response to stimulus defense response to other organism positive regulation of myeloid leukocyte mediated immunity positive regulation of defense response regulation of cell killing positive regulation of cell killing disruption of anatomical structure in another organism regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus positive regulation of killing of cells of another organism positive regulation of biological process biological process involved in symbiotic interaction positive regulation of response to stimulus neutrophil mediated immunity positive regulation of response to external stimulus regulation of response to stress positive regulation of neutrophil mediated killing of fungus positive regulation of immune effector process response to external biotic stimulus modulation of process of another organism positive regulation of cellular process regulation of biological process involved in symbiotic interaction neutrophil mediated cytotoxicity defense response regulation of neutrophil mediated cytotoxicity biological regulation regulation of leukocyte mediated cytotoxicity defense response to symbiont defense response to fungus killing by host of symbiont cells regulation of neutrophil mediated killing of symbiont cell cellular process response to fungus programmed cell death cell killing innate immune response ornithine metabolic process arginine catabolic process to ornithine catabolic process oxoacid metabolic process glutamine family amino acid catabolic process amino acid metabolic process arginine catabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process cellular catabolic process arginine metabolic process non-proteinogenic amino acid metabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process carboxylic acid metabolic process L-amino acid catabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process small molecule catabolic process negative regulation of lymphocyte proliferation regulation of leukocyte activation negative regulation of biological process regulation of cell activation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion negative regulation of cellular process regulation of multicellular organismal process regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of cell adhesion cell activation regulation of T cell activation negative regulation of cell activation regulation of T cell proliferation negative regulation of immune system process regulation of mononuclear cell proliferation regulation of lymphocyte activation response to nutrient levels response to lipid response to nutrient response to vitamin A response to vitamin regulation of localization import into cell nitrogen compound transport carboxylic acid transmembrane transport transport amino acid transmembrane transport L-amino acid transport localization regulation of amino acid transport regulation of amino acid transmembrane transport organic acid transmembrane transport organic anion transport carboxylic acid transport regulation of transport import across plasma membrane L-arginine import across plasma membrane establishment of localization regulation of L-arginine import across plasma membrane organic cation transport organic acid transport transmembrane transport amino acid transport amine transport regulation of amino acid import across plasma membrane regulation of transmembrane transport regulation of organic acid transport L-alpha-amino acid transmembrane transport regulation of amine transport amino acid import across plasma membrane cellular response to stimulus response to ketone cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to ketone cellular response to steroid hormone stimulus response to organic cyclic compound cellular response to hormone stimulus response to endogenous stimulus cellular response to dexamethasone stimulus response to glucocorticoid cellular response to organic cyclic compound cellular response to glucocorticoid stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to corticosteroid stimulus response to corticosteroid cellular response to chemical stimulus cellular response to lipid response to dexamethasone response to metal ion response to zinc ion defense response to protozoan response to protozoan response to type II interferon regulation of signal transduction regulation of type II interferon-mediated signaling pathway cellular response to type II interferon cell communication negative regulation of response to type II interferon interferon-mediated signaling pathway signal transduction regulation of innate immune response negative regulation of immune response type II interferon-mediated signaling pathway regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus negative regulation of response to external stimulus negative regulation of defense response regulation of immune response regulation of response to type II interferon negative regulation of response to biotic stimulus negative regulation of signaling signaling negative regulation of cell communication cytokine-mediated signaling pathway negative regulation of type II interferon-mediated signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus regulation of cytokine-mediated signaling pathway negative regulation of signal transduction negative regulation of cytokine-mediated signaling pathway regulation of cell communication negative regulation of innate immune response response to vitamin E nitrogen cycle metabolic process biosynthetic process urea cycle amide biosynthetic process amide metabolic process urea metabolic process multicellular organism development hepaticobiliary system development liver development system development response to acid chemical response to amino acid response to manganese ion response to peptide hormone response to nitrogen compound response to selenium ion regulation of activated T cell proliferation activated T cell proliferation negative regulation of activated T cell proliferation multi-multicellular organism process reproductive process female pregnancy multi-organism reproductive process cellular response to growth factor stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to growth factor cellular response to nitrogen compound cellular response to peptide hormone stimulus response to glucagon cellular response to glucagon stimulus maternal process involved in female pregnancy multicellular organismal reproductive process tube development respiratory tube development lung development respiratory system development cellular response to lipopolysaccharide cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to biotic stimulus response to bacterium response to molecule of bacterial origin collagen biosynthetic process collagen metabolic process cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to stress adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity T cell mediated immunity T-helper 2 cell cytokine production negative regulation of lymphocyte mediated immunity T cell cytokine production type 2 immune response regulation of T-helper 2 cell cytokine production cytokine production regulation of type 2 immune response negative regulation of T-helper 2 cell cytokine production regulation of T cell mediated immunity negative regulation of cytokine production involved in immune response regulation of cytokine production involved in immune response regulation of adaptive immune response negative regulation of metabolic process negative regulation of immune effector process negative regulation of adaptive immune response negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of gene expression negative regulation of type 2 immune response negative regulation of production of molecular mediator of immune response negative regulation of gene expression negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response negative regulation of T cell mediated immunity regulation of metabolic process negative regulation of T cell cytokine production regulation of T cell cytokine production CD4-positive, alpha-beta T cell cytokine production regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of cytokine production cytokine production involved in immune response negative regulation of macromolecule metabolic process production of molecular mediator of immune response regulation of biosynthetic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of lymphocyte mediated immunity negative regulation of biosynthetic process negative regulation of leukocyte mediated immunity response to herbicide response to toxic substance response to cadmium ion positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation response to amine	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane somatodendritic compartment cell body neuronal cell body extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR014033	Arginase	Family
A, B	IPR020855	Ureohydrolase, manganese-binding site	Binding Site
A, B	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily
A, B	IPR006035	Ureohydrolase	Family

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.