4YDY | pdb_00004ydy

CRYSTAL STRUCTURE OF DARPIN 44C12V5 IN COMPLEX WITH HUMAN IL-4

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B [auth I]	SCOP2B Superfamily	4-helical cytokines	8037758	3001717	SCOP2B (2022-06-29)
D [auth J]	SCOP2B Superfamily	4-helical cytokines	8037758	3001717	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	Flavodoxin_2	e4ydyA1	A: alpha bundles	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: Flavodoxin_2	ECOD (develop294)
C [auth B]	Flavodoxin_2	e4ydyB1	A: alpha bundles	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: Flavodoxin_2	ECOD (develop294)
B [auth I]	Nop10p	e4ydyI1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Nop10p	ECOD (develop294)
D [auth J]	Flavodoxin_2	e4ydyJ1	A: alpha bundles	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: Flavodoxin_2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)
C [auth B]	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)
B [auth I]	1.20.1250.10	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
D [auth J]	1.20.1250.10	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth I], D [auth J]	PF00727	Interleukin 4 (IL4)	Interleukin 4		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	DARPIN 44C12V5	-	-	-
B [auth I], D [auth J]	Interleukin-4	protein binding binding signaling receptor binding cytokine receptor binding interleukin-4 receptor binding growth factor receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity cytokine activity	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains response to stimulus regulation of leukocyte activation regulation of cell activation B cell activation involved in immune response positive regulation of macromolecule biosynthetic process regulation of primary metabolic process multicellular organism development positive regulation of immune response regulation of immune system process positive regulation of macromolecule metabolic process system development positive regulation of DNA recombination positive regulation of immunoglobulin mediated immune response adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains response to stimulus regulation of leukocyte activation regulation of cell activation B cell activation involved in immune response positive regulation of macromolecule biosynthetic process regulation of primary metabolic process multicellular organism development positive regulation of immune response regulation of immune system process positive regulation of macromolecule metabolic process system development positive regulation of DNA recombination positive regulation of immunoglobulin mediated immune response immune response DNA recombination primary metabolic process DNA metabolic process immune effector process regulation of gene expression biosynthetic process positive regulation of DNA metabolic process regulation of response to stimulus B cell mediated immunity positive regulation of production of molecular mediator of immune response regulation of macromolecule biosynthetic process metabolic process regulation of DNA metabolic process immunoglobulin production regulation of developmental process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains somatic cell DNA recombination somatic diversification of immunoglobulins involved in immune response positive regulation of lymphocyte activation somatic recombination of immunoglobulin gene segments positive regulation of biosynthetic process regulation of immunoglobulin mediated immune response regulation of B cell activation leukocyte activation involved in immune response positive regulation of isotype switching positive regulation of immune effector process positive regulation of cellular process production of molecular mediator of immune response positive regulation of immunoglobulin production regulation of isotype switching cell activation regulation of macromolecule metabolic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression immune system process somatic diversification of immune receptors via germline recombination within a single locus cellular process regulation of lymphocyte activation lymphocyte mediated immunity regulation of immune effector process multicellular organismal process regulation of DNA recombination positive regulation of leukocyte mediated immunity regulation of cellular process cell activation involved in immune response nucleobase-containing compound metabolic process positive regulation of developmental process positive regulation of cell activation positive regulation of metabolic process anatomical structure development positive regulation of leukocyte activation leukocyte mediated immunity somatic diversification of immune receptors regulation of nucleobase-containing compound metabolic process positive regulation of adaptive immune response positive regulation of immune system process somatic recombination of immunoglobulin genes involved in immune response developmental process regulation of biological process regulation of adaptive immune response regulation of B cell mediated immunity somatic diversification of immunoglobulins regulation of leukocyte mediated immunity regulation of immune response positive regulation of multicellular organismal process regulation of production of molecular mediator of immune response macromolecule metabolic process regulation of metabolic process isotype switching immune system development immunoglobulin production involved in immunoglobulin-mediated immune response positive regulation of lymphocyte mediated immunity positive regulation of biological process lymphocyte activation positive regulation of B cell mediated immunity leukocyte activation positive regulation of response to stimulus regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of isotype switching to IgG isotypes regulation of multicellular organismal process lymphocyte activation involved in immune response regulation of biosynthetic process B cell activation biological regulation gene expression adaptive immune response immunoglobulin mediated immune response positive regulation of B cell activation regulation of isotype switching to IgG isotypes regulation of lymphocyte mediated immunity regulation of immunoglobulin production isotype switching to IgG isotypes cellular response to growth factor stimulus negative regulation of response to stimulus regulation of cellular response to transforming growth factor beta stimulus cellular response to transforming growth factor beta stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus negative regulation of biological process negative regulation of cellular response to growth factor stimulus negative regulation of cellular response to transforming growth factor beta stimulus cellular response to endogenous stimulus response to transforming growth factor beta response to growth factor regulation of tumor necrosis factor production negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of metabolic process tumor necrosis factor superfamily cytokine production negative regulation of cytokine production tumor necrosis factor production negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production negative regulation of multicellular organismal process interleukin-13 production positive regulation of interleukin-13 production positive regulation of cytokine production regulation of interleukin-13 production regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response response to external stimulus regulation of inflammatory response response to stress negative regulation of response to external stimulus regulation of response to stress regulation of neuroinflammatory response negative regulation of defense response inflammatory response negative regulation of neuroinflammatory response neuroinflammatory response myeloid leukocyte differentiation regulation of leukocyte differentiation cellular developmental process cell development regulation of cell differentiation regulation of cell development regulation of osteoclast differentiation cell differentiation osteoclast differentiation negative regulation of cell differentiation negative regulation of hemopoiesis regulation of multicellular organismal development negative regulation of leukocyte differentiation hemopoiesis regulation of myeloid cell differentiation negative regulation of developmental process regulation of myeloid leukocyte differentiation negative regulation of myeloid cell differentiation negative regulation of osteoclast differentiation negative regulation of myeloid leukocyte differentiation negative regulation of cell development myeloid cell differentiation negative regulation of immune system process regulation of hemopoiesis leukocyte differentiation cellular response to stimulus cell surface receptor signaling pathway via STAT cell surface receptor signaling pathway signaling cell communication signal transduction cell surface receptor signaling pathway via JAK-STAT regulation of complement-dependent cytotoxicity negative regulation of complement-dependent cytotoxicity regulation of cell killing complement-dependent cytotoxicity negative regulation of cell killing cell killing negative regulation of locomotion regulation of cell motility tissue migration negative regulation of epithelial cell migration ameboidal-type cell migration regulation of cell migration cell migration epithelial cell migration cell motility regulation of epithelial cell migration locomotion negative regulation of cell migration epithelium migration regulation of locomotion negative regulation of cell motility regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport vesicle-mediated transport cellular component organization localization positive regulation of endocytosis cellular component organization or biogenesis positive regulation of receptor-mediated endocytosis regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of transport endocytosis receptor-mediated endocytosis type 2 immune response interleukin-10 production regulation of interleukin-10 production positive regulation of interleukin-10 production dendritic cell differentiation mononuclear cell differentiation macrophage activation myeloid leukocyte activation nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process positive regulation of phosphate metabolic process purine ribonucleoside triphosphate biosynthetic process positive regulation of nucleotide biosynthetic process regulation of nucleotide biosynthetic process regulation of ATP metabolic process ribonucleotide biosynthetic process purine nucleoside triphosphate biosynthetic process regulation of small molecule metabolic process positive regulation of purine nucleotide biosynthetic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process positive regulation of phosphorus metabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process ribonucleoside triphosphate biosynthetic process positive regulation of ATP metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process positive regulation of nucleotide metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process purine-containing compound biosynthetic process purine nucleoside triphosphate metabolic process carbohydrate derivative biosynthetic process regulation of purine nucleotide biosynthetic process nucleoside triphosphate biosynthetic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process positive regulation of purine nucleotide metabolic process positive regulation of ATP biosynthetic process regulation of ATP biosynthetic process organophosphate metabolic process positive regulation of small molecule metabolic process positive regulation of cell population proliferation positive regulation of B cell proliferation leukocyte proliferation regulation of B cell proliferation lymphocyte proliferation positive regulation of mononuclear cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation positive regulation of lymphocyte proliferation B cell proliferation regulation of cell population proliferation mononuclear cell proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II regulation of DNA-templated transcription negative regulation of RNA metabolic process T cell activation positive regulation of T cell activation positive regulation of T cell proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion regulation of cell-cell adhesion T cell proliferation positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation regulation of T cell proliferation positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process T cell mediated immunity T-helper 2 cell cytokine production T cell cytokine production regulation of T-helper 2 cell cytokine production regulation of type 2 immune response positive regulation of T cell cytokine production regulation of T cell mediated immunity regulation of cytokine production involved in immune response positive regulation of T-helper 2 cell cytokine production regulation of T cell cytokine production CD4-positive, alpha-beta T cell cytokine production cytokine production involved in immune response positive regulation of type 2 immune response positive regulation of T cell mediated immunity positive regulation of cytokine production involved in immune response lymphocyte differentiation B cell differentiation myeloid dendritic cell activation myeloid dendritic cell differentiation negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death positive regulation of amyloid-beta clearance amyloid-beta clearance regulation of amyloid-beta clearance regulation of isotype switching to IgE isotypes positive regulation of isotype switching to IgE isotypes isotype switching to IgE isotypes secondary alcohol metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process lipid metabolic process interleukin-4-mediated signaling pathway response to cytokine cytokine-mediated signaling pathway response to peptide response to interleukin-4 response to chemical cellular response to cytokine stimulus cellular response to interleukin-4 homeostatic process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of autophagy catabolic process macroautophagy autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process regulation of macroautophagy positive regulation of macroautophagy process utilizing autophagic mechanism positive regulation of locomotion positive regulation of cell migration positive regulation of cell motility regulation of MHC class II biosynthetic process MHC class II biosynthetic process positive regulation of MHC class II biosynthetic process negative regulation of endothelial cell apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic 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 positive regulation of cellular respiration positive regulation of T cell differentiation T cell differentiation positive regulation of cell development regulation of T cell differentiation positive regulation of hemopoiesis positive regulation of cell differentiation regulation of lymphocyte differentiation positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation	cellular anatomical structure extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth I], D [auth J]	IPR018096	Interleukin-4/interleukin-13, conserved site	Conserved Site
B [auth I], D [auth J]	IPR001325	Interleukin-4/interleukin-13	Family
B [auth I], D [auth J]	IPR002354	Interleukin-4	Family
B [auth I], D [auth J]	IPR009079	Four-helical cytokine-like, core	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth I], D [auth J]	Pharos: P05112	psoriasis allergic disease pneumonia autoimmune hepatitis adult T-cell leukemia/lymphoma asthma rhinitis cardiomyopathy autoimmune disease Drug Eruptions pleural disease cutaneous leishmaniasis pulmonary fibrosis bagassosis colitis psoriasis allergic disease pneumonia autoimmune hepatitis adult T-cell leukemia/lymphoma asthma rhinitis cardiomyopathy autoimmune disease Drug Eruptions pleural disease cutaneous leishmaniasis pulmonary fibrosis bagassosis colitis tuberculosis, bovine drug allergy malignant mesothelioma non-alcoholic fatty liver disease allergic contact dermatitis alopecia areata pneumoconiosis atopic eczema influenza kidney disease systemic lupus erythematosus common cold dermatitis, atopic acute T cell leukemia drug-induced liver injury arthritic joint disease Hodgkins lymphoma autism pustulosis palmaris et plantaris inborn carbohydrate metabolic disorder interstitial lung disease schizophrenia leishmaniasis tuberculosis liver disease lymphatic system disease obesity disorder allergic rhinitis pneumonitis hypereosinophilic syndrome idiopathic interstitial pneumonia inflammatory bowel disease dermatitis paranoid schizophrenia helminthiasis HIV infectious disease cancer

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.