3L5X

Crystal structure of the complex between IL-13 and H2L6 FAB

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth L]	d3l5xl2	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)
A [auth L]	d3l5xl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d3l5xh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d3l5xa_	All alpha proteins	4-helical cytokines	4-helical cytokines	Short-chain cytokines	Interleukin-13 (IL-13)	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)
C [auth A]	SCOP2B Superfamily	4-helical cytokines	8039590	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 [auth L]	PF07654	e3l5xL2	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)
A [auth L]	PF07686	e3l5xL1	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)
B [auth H]	PF07654	e3l5xH2	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	e3l5xH1	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 A]	PF03487	e3l5xA1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: 4-helical cytokines (From Topology)	T: 4-helical cytokines	F: PF03487	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth A]	1.20.1250.10	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	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 [auth L]	Anti-human IL-13 antibody H2L6 Fab	L-KAPPA	Homo sapiens (human)	IGKV3-1101, IGKJ201, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)
B [auth H]	Anti-human IL-13 antibody H2L6 Fab	VH-CH1	Homo sapiens (human)	IGHV2-509, IGHJ501, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L]	Light Chain	IGKV3	Kappa	interleukin-13	SAbDab (2024-04-26)
B [auth H]	Heavy Chain	IGHV2	-	interleukin-13	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF03487	Interleukin-13 (IL13)	Interleukin-13	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth L]	H2L6 LIGHT CHAIN	-	-	-
B [auth H]	H2L6 HEAVY CHAIN	-	-	-
C [auth A]	Interleukin-13	protein binding binding signaling receptor binding cytokine receptor binding interleukin-13 receptor binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity	multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process respiratory tube development regulation of cell differentiation negative regulation of lung ciliated cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation multicellular organism development cell differentiation anatomical structure development negative regulation of cellular process multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process respiratory tube development regulation of cell differentiation negative regulation of lung ciliated cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation multicellular organism development cell differentiation anatomical structure development negative regulation of cellular process lung development respiratory system development regulation of multicellular organismal process negative regulation of cell differentiation system development developmental process epithelium development regulation of biological process regulation of multicellular organismal development negative regulation of epithelial cell differentiation lung ciliated cell differentiation tube development negative regulation of developmental process biological regulation animal organ development regulation of lung ciliated cell differentiation lung epithelium development tissue development lung epithelial cell differentiation lung cell differentiation cellular process negative regulation of multicellular organismal process regulation of transforming growth factor beta production cellular biosynthetic process negative regulation of cellular metabolic process organic substance metabolic process regulation of cytokine production organic substance biosynthetic process cytokine production transforming growth factor beta production negative regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process negative regulation of transforming growth factor beta production regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of localization regulation of proton transport transport regulation of transport proton transmembrane transport monoatomic ion transmembrane transport regulation of monoatomic ion transport inorganic ion transmembrane transport regulation of monoatomic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization regulation of transmembrane transport monoatomic ion transport regulation of monoatomic cation transmembrane transport monoatomic cation transport regulation of macrophage activation positive regulation of macrophage activation regulation of leukocyte activation cell activation positive regulation of biological process regulation of cell activation myeloid leukocyte activation leukocyte activation macrophage activation positive regulation of cell activation immune system process positive regulation of leukocyte activation positive regulation of multicellular organismal process regulation of immune system process positive regulation of immune system process positive regulation of cellular process response to stimulus immune response lobar bronchus epithelium development lung secretory cell differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of lung goblet cell differentiation bronchus development lobar bronchus development lung goblet cell differentiation positive regulation of epithelial cell differentiation glandular epithelial cell differentiation positive regulation of lung goblet cell differentiation columnar/cuboidal epithelial cell differentiation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of gene expression positive regulation of cellular biosynthetic process establishment of organelle localization regulation of immune effector process regulated exocytosis regulation of myeloid leukocyte mediated immunity cell activation involved in immune response leukocyte degranulation myeloid leukocyte mediated immunity vesicle-mediated transport positive regulation of leukocyte degranulation positive regulation of regulated secretory pathway establishment of localization in cell leukocyte mediated immunity positive regulation of mast cell degranulation vacuolar localization mast cell degranulation immune effector process regulation of secretion regulation of leukocyte mediated immunity exocytosis lysosome localization cellular localization positive regulation of secretion by cell positive regulation of exocytosis regulation of mast cell degranulation regulation of regulated secretory pathway secretion by cell regulation of secretion by cell positive regulation of secretion organelle localization leukocyte activation involved in immune response mast cell activation positive regulation of immune effector process regulation of leukocyte degranulation mast cell mediated immunity secretion export from cell regulation of vesicle-mediated transport myeloid cell activation involved in immune response mast cell activation involved in immune response positive regulation of transport regulation of exocytosis regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response regulation of connective tissue growth factor production connective tissue growth factor production positive regulation of cytokine production positive regulation of connective tissue growth factor production response to organic substance response to alcohol response to chemical response to oxygen-containing compound response to ethanol 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 homeostatic process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis protein localization establishment of protein localization nitrogen compound transport regulation of protein localization positive regulation of establishment of protein localization protein localization to extracellular region positive regulation of protein transport cellular macromolecule localization organic substance transport regulation of establishment of protein localization establishment of protein localization to extracellular region regulation of protein transport protein secretion positive regulation of protein secretion regulation of protein secretion protein transport regulation of cellular localization macromolecule localization positive regulation of protein localization cellular response to stimulus response to mechanical stimulus response to abiotic stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus immunoglobulin production positive regulation of immunoglobulin production production of molecular mediator of immune response regulation of immunoglobulin production positive regulation of production of molecular mediator of immune response regulation of production of molecular mediator of immune response positive regulation of phosphorylation positive regulation of phosphate metabolic process cell communication regulation of primary metabolic process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process signal transduction protein modification process phosphorus metabolic process positive regulation of protein phosphorylation tyrosine phosphorylation of STAT protein protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process primary metabolic process macromolecule modification regulation of phosphorus metabolic process cell surface receptor signaling pathway via STAT regulation of protein modification process signaling regulation of protein phosphorylation positive regulation of protein metabolic process peptidyl-tyrosine modification positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process protein metabolic process organonitrogen compound metabolic process cell surface receptor signaling pathway regulation of tyrosine phosphorylation of STAT protein regulation of peptidyl-tyrosine phosphorylation positive regulation of tyrosine phosphorylation of STAT protein regulation of phosphorylation peptidyl-tyrosine phosphorylation cell surface receptor signaling pathway via JAK-STAT interleukin-10 production regulation of interleukin-10 production positive regulation of interleukin-10 production cell population proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation regulation of calcium ion transport positive regulation of cation transmembrane transport positive regulation of calcium ion transport intracellular calcium ion homeostasis calcium ion transport positive regulation of monoatomic ion transport positive regulation of monoatomic ion transmembrane transport monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of release of sequestered calcium ion into cytosol maintenance of location release of sequestered calcium ion into cytosol chemical homeostasis inorganic ion homeostasis calcium ion homeostasis negative regulation of sequestering of calcium ion metal ion transport maintenance of location in cell regulation of calcium ion transmembrane transport intracellular monoatomic cation homeostasis monoatomic ion homeostasis positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport intracellular chemical homeostasis positive regulation of release of sequestered calcium ion into cytosol regulation of metal ion transport regulation of sequestering of calcium ion calcium ion transmembrane import into cytosol sequestering of calcium ion cellular homeostasis calcium ion transmembrane transport positive regulation of B cell proliferation lymphocyte activation leukocyte proliferation positive regulation of lymphocyte activation regulation of B cell proliferation lymphocyte proliferation regulation of B cell activation positive regulation of mononuclear cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation B cell activation positive regulation of lymphocyte proliferation B cell proliferation positive regulation of B cell activation mononuclear cell proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation negative regulation of endothelial cell apoptotic process regulation of epithelial cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death epithelial cell apoptotic process negative regulation of apoptotic process negative regulation of epithelial cell apoptotic process endothelial cell apoptotic process apoptotic process programmed cell death regulation of endothelial cell apoptotic process response to nicotine positive regulation of pancreatic stellate cell proliferation fibroblast proliferation pancreatic stellate cell proliferation regulation of fibroblast proliferation positive regulation of fibroblast proliferation regulation of pancreatic stellate cell proliferation biological process involved in interspecies interaction between organisms response to lipid response to other organism response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin leukocyte activation involved in inflammatory response microglial cell activation glial cell activation neuroinflammatory response cellular response to chemical stimulus response to cytokine cellular response to cytokine stimulus cellular response to organic substance	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane intracellular anatomical structure cytoplasm extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR001325	Interleukin-4/interleukin-13	Family
C [auth A]	IPR018096	Interleukin-4/interleukin-13, conserved site	Conserved Site
C [auth A]	IPR020470	Interleukin-13	Family
C [auth A]	IPR009079	Four-helical cytokine-like, core	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A]	Pharos: P35225	allergic rhinitis psoriasis atopic eczema allergic disease autoimmune hepatitis renal cell carcinoma asthma pneumonia sinusitis Hodgkins lymphoma hyperplasia Arthritis, Experimental lung disease papillary renal cell carcinoma chromophobe renal cell carcinoma allergic rhinitis psoriasis atopic eczema allergic disease autoimmune hepatitis renal cell carcinoma asthma pneumonia sinusitis Hodgkins lymphoma hyperplasia Arthritis, Experimental lung disease papillary renal cell carcinoma chromophobe renal cell carcinoma sarcomatoid renal cell carcinoma psoriatic arthritis drug allergy alopecia areata collecting duct carcinoma pulmonary fibrosis dermatitis renal carcinoma sarcoidosis helminthiasis arthritic joint disease idiopathic interstitial pneumonia inflammatory bowel disease autism common cold dermatitis, atopic Huntington disease inherited susceptibility to asthma clear cell renal carcinoma pustulosis palmaris et plantaris rhinitis hypereosinophilic syndrome autoimmune disease cancer pneumonitis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth H]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.