6JWN | pdb_00006jwn

Crystal structure of the SPRY domain of SPSB2 in complex with cR9, a cyclic peptide inhibitor of SPSB-iNOS interaction

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8059603	3000120	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8059603	3000120	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	SPRY	e6jwnA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)
C	SPRY	e6jwnC1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: SPRY	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00622	SPRY domain (SPRY)	SPRY domain	SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of ...	SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of histone H3 methylation, innate immunity or embryonic development [1,2,3,4]. It can be divided into 11 subfamilies based on amino acid sequence similarity or the presence of additional protein domains. The greater SPRY family is divided into the SPRY/B30.2 (which contains a PRY extension at the N-terminal) and SPRY-only sub-families which are preceded by a subdomain that is structurally similar to the PRY region [2]. SPRY/B30.2 structures revealed a bent beta-sandwich fold comprised of two beta-sheets. Distant homologues are domains in butyrophilin/ marenostrin/pyrin [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	SPRY domain-containing SOCS box protein 2	ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process cellular response to stimulus catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation signal transduction intracellular signal transduction cell communication protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex
B, D	Nitric oxide synthase, inducible	FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding flavin adenine dinucleotide binding cation binding organic acid binding amino acid binding FMN binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding flavin adenine dinucleotide binding cation binding organic acid binding amino acid binding carboxylic acid binding arginine binding oxidoreductase activity monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen nitric-oxide synthase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen catalytic activity protein binding calmodulin binding metal ion binding tetrahydrobiopterin binding purine nucleotide binding adenyl nucleotide binding NADP binding identical protein binding protein homodimerization activity protein dimerization activity tetrapyrrole binding heme binding	prostaglandin transport transport signaling cell communication localization secretion by cell monocarboxylic acid transport fatty acid transport icosanoid transport signal release prostaglandin secretion icosanoid secretion regulation of biological process organic anion transport prostaglandin transport transport signaling cell communication localization secretion by cell monocarboxylic acid transport fatty acid transport icosanoid transport signal release prostaglandin secretion icosanoid secretion regulation of biological process organic anion transport carboxylic acid transport secretion biological regulation cell-cell signaling export from cell lipid localization lipid transport establishment of localization organic acid transport lipid export from cell macromolecule localization cellular process catabolic process oxoacid metabolic process carboxylic acid metabolic process L-amino acid catabolic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid catabolic process alpha-amino acid metabolic process L-amino acid metabolic process glutamine family amino acid metabolic process proteinogenic amino acid metabolic process arginine metabolic process L-arginine catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process metabolic process small molecule metabolic process small molecule catabolic process amino acid catabolic process defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus peptidyl-cysteine modification peptidyl-cysteine S-nitrosylation macromolecule modification peptidyl-amino acid modification protein metabolic process macromolecule metabolic process protein modification process protein nitrosylation multicellular organismal process regulation of cellular process positive regulation of interleukin-8 production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of multicellular organismal process positive regulation of cellular process regulation of biosynthetic process interleukin-8 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of metabolic process regulation of interleukin-8 production regulation of localization establishment of protein localization nitrogen compound transport regulation of hormone secretion regulation of protein localization regulation of peptide secretion hormone secretion protein localization to extracellular region peptide secretion regulation of secretion by cell amide transport intracellular protein localization regulation of biological quality regulation of peptide hormone secretion regulation of signaling regulation of transport regulation of hormone levels regulation of peptide transport regulation of establishment of protein localization establishment of protein localization to extracellular region regulation of protein transport protein secretion regulation of protein secretion regulation of secretion peptide transport protein transport regulation of insulin secretion peptide hormone secretion hormone transport regulation of cell communication insulin secretion cell redox homeostasis cellular homeostasis homeostatic process response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus defense response to Gram-negative bacterium cellular response to stimulus cellular response to chemical stimulus response to chemical cellular response to xenobiotic stimulus response to xenobiotic stimulus negative regulation of biological process macromolecule catabolic process negative regulation of protein catabolic process regulation of primary metabolic process negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of protein metabolic process negative regulation of metabolic process protein catabolic process regulation of catabolic process regulation of protein catabolic process response to hormone response to endogenous stimulus rhythmic process circadian rhythm nitric oxide mediated signal transduction intracellular signal transduction intracellular signaling cassette signal transduction superoxide metabolic process reactive oxygen species metabolic process interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production response to lipid cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to biotic stimulus cellular response to lipid response to molecule of bacterial origin regulation of immune effector process positive regulation of leukocyte mediated immunity regulation of leukocyte mediated cytotoxicity leukocyte mediated cytotoxicity immune effector process regulation of leukocyte mediated immunity positive regulation of leukocyte mediated cytotoxicity immune system process leukocyte mediated immunity regulation of immune system process regulation of cell killing positive regulation of immune effector process positive regulation of cell killing positive regulation of immune system process cell killing immune response response to type II interferon response to cytokine defense response to symbiont cellular response to type II interferon response to peptide defense response to other organism innate immune response cellular response to cytokine stimulus innate immune response in mucosa mucosal immune response organ or tissue specific immune response regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response cytokine production involved in inflammatory response inflammatory response cell population proliferation regulation of cell population proliferation negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process cellular respiration energy derivation by oxidation of organic compounds regulation of generation of precursor metabolites and energy generation of precursor metabolites and energy regulation of cellular respiration immune response-regulating cell surface receptor signaling pathway involved in phagocytosis import into cell immune response-regulating cell surface receptor signaling pathway Fc-gamma receptor signaling pathway involved in phagocytosis vesicle-mediated transport positive regulation of response to stimulus immune response-activating signaling pathway Fc receptor signaling pathway immune response-regulating signaling pathway positive regulation of immune response phagocytosis Fc-gamma receptor signaling pathway cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway Fc receptor mediated stimulatory signaling pathway regulation of response to stimulus regulation of immune response endocytosis activation of immune response system process circulatory system process regulation of blood pressure negative regulation of blood pressure blood circulation nitric oxide metabolic process nitric oxide biosynthetic process reactive nitrogen species metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle peroxisome microbody intracellular membrane-bounded organelle perinuclear region of cytoplasm peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle peroxisome microbody intracellular membrane-bounded organelle perinuclear region of cytoplasm peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen organelle lumen microbody lumen cell cortex cortical cytoskeleton intracellular membraneless organelle cell periphery cytoskeleton membraneless organelle plasma membrane membrane nucleus nucleoplasm nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR001870	B30.2/SPRY domain	Domain
A, C	IPR036036	SOCS box-like domain superfamily	Homologous Superfamily
A, C	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, C	IPR001496	SOCS box domain	Domain
A, C	IPR050672	F-box/SPRY and SOCS box protein families	Family
A, C	IPR043136	B30.2/SPRY domain superfamily	Homologous Superfamily
A, C	IPR037340	SSB2, SOCS box domain	Domain
A, C	IPR003877	SPRY domain	Domain
B, D	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase	Domain
B, D	IPR001433	Oxidoreductase FAD/NAD(P)-binding	Domain
B, D	IPR001094	Flavodoxin-like	Domain
B, D	IPR004030	Nitric oxide synthase, N-terminal	Domain
B, D	IPR023173	NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily	Homologous Superfamily
B, D	IPR008254	Flavodoxin/nitric oxide synthase	Domain
B, D	IPR039261	Ferredoxin-NADP reductase (FNR), nucleotide-binding domain	Homologous Superfamily
B, D	IPR017927	FAD-binding domain, ferredoxin reductase-type	Domain
B, D	IPR036119	Nitric oxide synthase, N-terminal domain superfamily	Homologous Superfamily
B, D	IPR044944	Nitric oxide synthase, domain 3 superfamily	Homologous Superfamily
B, D	IPR044943	Nitric oxide synthase, domain 1 superfamily	Homologous Superfamily
B, D	IPR003097	Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding	Domain
B, D	IPR017938	Riboflavin synthase-like beta-barrel	Homologous Superfamily
B, D	IPR044940	Nitric oxide synthase, domain 2 superfamily	Homologous Superfamily
B, D	IPR029039	Flavoprotein-like superfamily	Homologous Superfamily
B, D	IPR050607	Nitric Oxide Synthase (NOS)	Family
B, D	IPR012144	Nitric-oxide synthase, eukaryote	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: Q99619	colorectal cancer ovarian cancer pituitary cancer
B, D	Pharos: P35228	psoriasis hypertensive disorder Marfan syndrome sclerosing cholangitis silicosis Stevens-Johnson syndrome duodenal ulcer Turner syndrome status epilepticus malaria psoriatic arthritis Takayasu arteritis cholangiocarcinoma asbestosis asthma psoriasis hypertensive disorder Marfan syndrome sclerosing cholangitis silicosis Stevens-Johnson syndrome duodenal ulcer Turner syndrome status epilepticus malaria psoriatic arthritis Takayasu arteritis cholangiocarcinoma asbestosis asthma liver disease congestive heart failure visual epilepsy malignant colon neoplasm primary sclerosing cholangitis Hyperalgesia breast carcinoma substance withdrawal syndrome essential hypertension toxic shock syndrome myocardial infarction intestinal schistosomiasis cholestasis focal segmental glomerulosclerosis aspiration pneumonia perinatal necrotizing enterocolitis brain ischemia bronchial disease retinal disease secondary Parkinson disease intestinal disease intrahepatic cholangiocarcinoma ureteral obstruction gastric ulcer kidney disease colitis atherosclerosis brain edema subarachnoid hemorrhage manganese poisoning esophageal cancer type 2 diabetes mellitus myocardial stunning heart failure lung carcinoma Crohn disease brain hypoxia - ischemia pulmonary emphysema acute kidney failure pustulosis palmaris et plantaris extrahepatic cholestasis ulcerative colitis chronic obstructive pulmonary disease neoplasm of esophagus benign colon neoplasm sinusitis primary biliary cholangitis bowel dysfunction maturity-onset diabetes of the young essential hypertension, genetic cerebrovascular disorder arteriosclerosis disorder aspiration pneumonitis autism lung benign neoplasm bile duct cancer cystic fibrosis primary ovarian failure depressive disorder breast cancer burn ankylosing spondylitis inborn mitochondrial metabolism disorder toxic epidermal necrolysis ischemia reperfusion injury urinary tract infection necrotizing enterocolitis colonic neoplasm