3NFP

Crystal structure of the Fab fragment of therapeutic antibody daclizumab in complex with IL-2Ra (CD25) ectodomain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3nfpa_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth H]	d3nfph_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3nfpb2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3nfpb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth L]	d3nfpl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth L]	d3nfpl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth I]	d3nfpi1	Small proteins	Complement control module/SCR domain	Complement control module/SCR domain	Complement control module/SCR domain	Interleukin-2 receptor alpha chain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth K]	d3nfpk1	Small proteins	Complement control module/SCR domain	Complement control module/SCR domain	Complement control module/SCR domain	Interleukin-2 receptor alpha chain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth I]	SCOP2B Superfamily	Sushi/CCP/SCR domain	8037668	3000902	SCOP2B (2022-06-29)
E [auth I]	SCOP2B Superfamily	Sushi/CCP/SCR domain	8037669	3000902	SCOP2B (2022-06-29)
F [auth K]	SCOP2B Superfamily	Sushi/CCP/SCR domain	8037668	3000902	SCOP2B (2022-06-29)
F [auth K]	SCOP2B Superfamily	Sushi/CCP/SCR domain	8037669	3000902	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	V-set_8	e3nfpA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
A	C1-set_1	e3nfpA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C [auth H]	V-set_8	e3nfpH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth H]	C1-set_1	e3nfpH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
B	C1-set_4	e3nfpB6	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B	V-set	e3nfpB5	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
D [auth L]	C1-set_4	e3nfpL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
D [auth L]	V-set	e3nfpL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
E [auth I]	Sushi_4	e3nfpI1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: Complement control module/SCR domain	F: Sushi_4	ECOD (1.6)
E [auth I]	Sushi_3	e3nfpI2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: Complement control module/SCR domain	F: Sushi_3	ECOD (1.6)
F [auth K]	Sushi_4	e3nfpK3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: Complement control module/SCR domain	F: Sushi_4	ECOD (1.6)
F [auth K]	Sushi_3	e3nfpK4	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: Complement control module/SCR domain	F: Sushi_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth I]	2.10.70.10	Mainly Beta	Ribbon	Complement Module	domain 1	CATH (4.3.0)
E [auth I]	2.20.28.230	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)
F [auth K]	2.10.70.10	Mainly Beta	Ribbon	Complement Module	domain 1	CATH (4.3.0)
F [auth K]	2.20.28.230	Mainly Beta	Single Sheet	Rubrerythrin, domain 2		CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A, C [auth H]	daclizumab Fab	VH-CH1	Homo sapiens (human)	IGHV1-4601, IGHV1-4603, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG1*05	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202448-0)
B, D [auth L]	daclizumab Fab	L-KAPPA	Homo sapiens (human)	IGKV1-501, IGKV1-503, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202448-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, C [auth H]	Heavy Chain	IGHV1	-	interleukin-2 receptor subunit alpha	SAbDab (2024-12-06)
B, D [auth L]	Light Chain	IGKV1	Kappa	interleukin-2 receptor subunit alpha	SAbDab (2024-12-06)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A, C [auth H]	Daclizumab	IL2RA/CD25	Therapeutic SAbDab (2024-12-06)
B, D [auth L]	Daclizumab	IL2RA/CD25	Therapeutic SAbDab (2024-12-06)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth I], F [auth K]	PF00084	Sushi repeat (SCR repeat) (Sushi)	Sushi repeat (SCR repeat)	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth H]	Heavy chain of Fab fragment of daclizumab	-	-	-
B, D [auth L]	Light chain of Fab fragment of daclizumab	-	-	-
E [auth I], F [auth K]	Interleukin-2 receptor subunit alpha	protein binding binding growth factor binding cytokine binding interleukin-2 binding molecular transducer activity interleukin-2 receptor activity transmembrane signaling receptor activity signaling receptor activity cytokine receptor activity immune receptor activity	multicellular organismal process regulation of cellular process positive regulation of cell population proliferation regulation of leukocyte activation regulation of cell activation positive regulation of cell activation T cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of immune system process positive regulation of immune system process regulation of leukocyte proliferation regulation of biological process cell population proliferation multicellular organismal process regulation of cellular process positive regulation of cell population proliferation regulation of leukocyte activation regulation of cell activation positive regulation of cell activation T cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of immune system process positive regulation of immune system process regulation of leukocyte proliferation regulation of biological process cell population proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of activated T cell proliferation regulation of cell population proliferation mononuclear cell proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of multicellular organismal process regulation of activated T cell proliferation positive regulation of biological process positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation activated T cell proliferation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of mononuclear cell proliferation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of cellular process T cell proliferation regulation of lymphocyte proliferation positive regulation of cell adhesion regulation of cell adhesion biological regulation cell activation regulation of T cell activation regulation of T cell proliferation immune system process regulation of mononuclear cell proliferation cellular process regulation of lymphocyte activation regulation of alpha-beta T cell activation regulation of alpha-beta T cell proliferation alpha-beta T cell proliferation CD4-positive, alpha-beta T cell activation alpha-beta T cell activation CD4-positive, alpha-beta T cell proliferation regulation of CD4-positive, alpha-beta T cell proliferation regulation of CD4-positive, alpha-beta T cell activation cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling signal transduction cell communication defense response immune response response to stress inflammatory response inflammatory response to antigenic stimulus interleukin-2-mediated signaling pathway cellular response to interleukin-2 response to cytokine cytokine-mediated signaling pathway response to peptide response to interleukin-2 response to chemical cellular response to cytokine stimulus homeostatic process T cell homeostatic proliferation T cell homeostasis multicellular organismal-level homeostasis regulation of T cell homeostatic proliferation leukocyte homeostasis homeostasis of number of cells lymphocyte homeostasis apoptotic process cell death programmed cell death regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response negative regulation of response to stimulus negative regulation of biological process response to external stimulus regulation of inflammatory response regulation of response to stimulus negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response immune system development developmental process T cell tolerance induction multicellular organism development anatomical structure development regulation of tolerance induction regulation of T cell tolerance induction tolerance induction system development negative regulation of lymphocyte proliferation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation negative regulation of lymphocyte activation negative regulation of mononuclear cell proliferation negative regulation of cellular process negative regulation of cell population proliferation negative regulation of cell activation negative regulation of immune system process Notch signaling pathway leukocyte apoptotic process lymphocyte apoptotic process activation-induced cell death of T cells T cell apoptotic process regulation of leukocyte differentiation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation positive regulation of T cell differentiation regulation of cell development positive regulation of developmental process cell differentiation T cell differentiation positive regulation of cell development leukocyte differentiation cellular developmental process regulation of developmental process cell development regulation of T cell differentiation positive regulation of hemopoiesis positive regulation of cell differentiation regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex interleukin-2 receptor complex receptor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth I], F [auth K]	IPR015486	Interleukin-2 receptor alpha	Family
E [auth I], F [auth K]	IPR000436	Sushi/SCR/CCP domain	Domain
E [auth I], F [auth K]	IPR035976	Sushi/SCR/CCP superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth I], F [auth K]	Pharos: P01589	rheumatoid arthritis immunodeficiency due to CD25 deficiency Crohn disease alopecia areata HIV infectious disease juvenile idiopathic arthritis type 1 diabetes mellitus glomerulonephritis type 1 diabetes mellitus 10 multiple sclerosis oligoarticular juvenile idiopathic arthritis malignant mesothelioma chronic beryllium disease schizophrenia allergic contact dermatitis rheumatoid arthritis immunodeficiency due to CD25 deficiency Crohn disease alopecia areata HIV infectious disease juvenile idiopathic arthritis type 1 diabetes mellitus glomerulonephritis type 1 diabetes mellitus 10 multiple sclerosis oligoarticular juvenile idiopathic arthritis malignant mesothelioma chronic beryllium disease schizophrenia allergic contact dermatitis Regional enteritis sclerosing cholangitis Graves disease acquired metabolic disease allergic rhinitis atopic eczema major depressive disorder psoriasis relapsing-remitting multiple sclerosis rheumatoid factor-negative juvenile idiopathic arthritis glioblastoma Hashimoto thyroiditis vitiligo hypothyroidism acute myeloid leukemia inflammatory bowel disease large cell medulloblastoma atypical teratoid rhabdoid tumor neuroblastoma ovarian cancer Crohn's colitis diabetes mellitus ileocolitis interstitial cystitis asthma lung adenocarcinoma autoimmune disease marginal zone lymphoma common variable immunodeficiency non-small cell lung carcinoma primary cutaneous T-cell lymphoma

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.