2XQB

Crystal Structure of anti-IL-15 Antibody in Complex with human IL-15

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
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	d2xqba_	All alpha proteins	4-helical cytokines	4-helical cytokines	Short-chain cytokines	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d2xqbh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d2xqbl2	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)
C [auth L]	d2xqbl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	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)
A	SCOP2B Superfamily	4-helical cytokines	8038027	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	PF02372	e2xqbA1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: 4-helical cytokines (From Topology)	T: 4-helical cytokines	F: PF02372	ECOD (1.6)
B [auth H]	PF07654	e2xqbH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B [auth H]	PF07686	e2xqbH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth L]	PF07654	e2xqbL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C [auth L]	PF07686	e2xqbL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1250.70	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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
B [auth H]	DISC0280 Fab, anti-IL-15	VH-CH1	Homo sapiens (human)	IGHV1-1801, IGHV1-1804, IGHJ502, IGHG103	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202416-0)
C [auth L]	DISC0280 Fab, anti-IL-15	L-LAMBDA	Homo sapiens (human)	IGLV1-4701, IGLJ201, IGLJ302, IGLJ301, IGLC201, IGLC202, IGLC3*04	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV1	-	interleukin 15	SAbDab (2024-04-26)
C [auth L]	Light Chain	IGLV1	Lambda	interleukin 15	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02372	Interleukin 15 (IL15)	Interleukin 15	Interleukin-15 (IL-15) is a cytokine that possesses a variety of biological functions, including stimulation and maintenance of cellular immune responses [1]. Structurally these proteins are short-chain 4-helical cytokines.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	INTERLEUKIN 15	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity cytokine receptor binding	regulation of defense response regulation of response to biotic stimulus regulation of biological process biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus response to other organism defense response biological regulation defense response to symbiont response to external stimulus response to biotic stimulus regulation of defense response to virus defense response to virus regulation of response to stimulus regulation of defense response regulation of response to biotic stimulus regulation of biological process biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus response to other organism defense response biological regulation defense response to symbiont response to external stimulus response to biotic stimulus regulation of defense response to virus defense response to virus regulation of response to stimulus defense response to other organism response to stress regulation of response to stress regulation of defense response to virus by host response to external biotic stimulus response to virus immune response positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response immune system process regulation of immune response regulation of immune system process positive regulation of immune system process cellular response to stimulus cell surface receptor signaling pathway via STAT regulation of cellular process signaling peptidyl-tyrosine modification cell communication organic substance metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process signal transduction protein modification process phosphorus metabolic process tyrosine phosphorylation of STAT protein organonitrogen compound metabolic process protein phosphorylation cell surface receptor signaling pathway phosphorylation cellular metabolic process primary metabolic process macromolecule modification metabolic process cellular process macromolecule metabolic process peptidyl-tyrosine phosphorylation cell surface receptor signaling pathway via JAK-STAT developmental process immune system development multicellular organism development multicellular organismal process lymph node development animal organ development anatomical structure development hematopoietic or lymphoid organ development system development regulation of inflammatory response positive regulation of response to external stimulus positive regulation of inflammatory response positive regulation of defense response inflammatory response positive regulation of glycoprotein metabolic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of protein metabolic process glycoprotein biosynthetic process regulation of cellular metabolic process glycoprotein metabolic process regulation of glycoprotein metabolic process biosynthetic process protein O-linked glycosylation regulation of protein glycosylation regulation of macromolecule biosynthetic process regulation of metabolic process regulation of protein modification process cellular biosynthetic process positive regulation of protein metabolic process positive regulation of cellular metabolic process positive regulation of protein glycosylation regulation of protein O-linked glycosylation positive regulation of protein modification process positive regulation of biosynthetic process regulation of glycoprotein biosynthetic process positive regulation of cellular process positive regulation of glycoprotein biosynthetic process carbohydrate derivative biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process protein glycosylation macromolecule biosynthetic process regulation of cellular biosynthetic process glycosylation positive regulation of protein O-linked glycosylation macromolecule glycosylation positive regulation of cellular biosynthetic process neutrophil activation cell activation myeloid leukocyte activation granulocyte activation leukocyte activation cell population proliferation lymphocyte activation NK T cell proliferation leukocyte proliferation NK T cell activation T cell activation alpha-beta T cell proliferation mononuclear cell proliferation lymphocyte proliferation alpha-beta T cell activation T cell proliferation cell-cell signaling 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 phagocytosis cellular component organization or biogenesis regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of phagocytosis positive regulation of transport endocytosis positive regulation of cell population proliferation regulation of leukocyte activation regulation of cell activation positive regulation of natural killer cell proliferation positive regulation of lymphocyte activation positive regulation of cell activation positive regulation of leukocyte activation positive regulation of mononuclear cell proliferation regulation of multicellular organismal process regulation of natural killer cell activation regulation of lymphocyte proliferation regulation of leukocyte proliferation positive regulation of lymphocyte proliferation positive regulation of natural killer cell activation natural killer cell activation natural killer cell proliferation regulation of cell population proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation positive regulation of multicellular organismal process regulation of lymphocyte activation regulation of natural killer cell proliferation regulation of leukocyte differentiation cellular developmental process regulation of developmental process cell development mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation regulation of cell development regulation of T cell differentiation cell differentiation T cell differentiation regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis regulation of T cell activation regulation of hemopoiesis leukocyte differentiation anatomical structure maturation cell maturation developmental maturation interleukin-15-mediated signaling pathway response to organic substance response to cytokine cellular response to interleukin-15 cytokine-mediated signaling pathway cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular response to organic substance response to interleukin-15 positive regulation of developmental process natural killer cell differentiation positive regulation of cell development regulation of natural killer cell differentiation positive regulation of hemopoiesis positive regulation of cell differentiation positive regulation of natural killer cell differentiation positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation positive regulation of tissue remodeling tissue remodeling regulation of tissue remodeling extrathymic T cell selection extrathymic T cell differentiation T cell selection myeloid leukocyte differentiation macrophage differentiation myeloid cell differentiation positive regulation of phosphorylation positive regulation of phosphate metabolic process regulation of phosphate metabolic process positive regulation of protein phosphorylation positive regulation of phosphorus metabolic process regulation of phosphorus metabolic process regulation of protein phosphorylation positive regulation of peptidyl-tyrosine phosphorylation regulation of tyrosine phosphorylation of STAT protein regulation of peptidyl-tyrosine phosphorylation positive regulation of tyrosine phosphorylation of STAT protein regulation of phosphorylation cytokine production regulation of cytokine production interleukin-17 production gene expression regulation of gene expression regulation of interleukin-17 production positive regulation of gene expression positive regulation of interleukin-17 production positive regulation of cytokine production negative regulation of cold-induced thermogenesis homeostatic process negative regulation of metabolic process negative regulation of biological process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis negative regulation of multicellular organismal process 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 positive regulation of cell adhesion regulation of cell adhesion regulation of T cell proliferation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cytoplasm cytosol Golgi apparatus endomembrane system endosome intracellular vesicle cytoplasmic vesicle vesicle extracellular region extracellular space
B [auth H]	ANTI-IL-15 ANTIBODY	-	-	-
C [auth L]	ANTI-IL-15 ANTIBODY	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003443	Interleukin-15/Interleukin-21 family	Family
A	IPR020439	Interleukin-15	Family
A	IPR020466	Interleukin-15, mammal	Family
A	IPR009079	Four-helical cytokine-like, core	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P40933	polyomavirus infectious disease celiac disease Respiratory Hypersensitivity endometriosis non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm transitional cell carcinoma arthritic joint disease autoimmune disease hematologic disease malignant colon neoplasm malignant mesothelioma osteosarcoma pilocytic astrocytoma tuberculosis polyomavirus infectious disease celiac disease Respiratory Hypersensitivity endometriosis non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm transitional cell carcinoma arthritic joint disease autoimmune disease hematologic disease malignant colon neoplasm malignant mesothelioma osteosarcoma pilocytic astrocytoma tuberculosis autism breast cancer Crohn disease lung cancer malignant ependymoma nasopharyngeal carcinoma ovarian cancer plasma cell myeloma sarcoidosis ulcerative colitis cancer cutaneous lupus erythematosus glioblastoma lymphatic system disease malignant glioma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.