3KR3

Crystal structure of IGF-II antibody complex

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth D]	d3kr3d_	Small proteins	Insulin-like	Insulin-like	Insulin-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d3kr3l2	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]	d3kr3l1	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 [auth D]	SCOP2 Family	Insulin-like	8070330	4003135	SCOP2 (2022-06-29)
A [auth D]	SCOP2 Superfamily	Insulin-like	8070331	3000307	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth H]	C1-set_1	e3kr3H2	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 [auth H]	V-set_12	e3kr3H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
A [auth D]	Insulin	e3kr3D1	A: few secondary structure elements	X: Insulin-like (From Topology)	H: Insulin-like (From Topology)	T: Insulin-like	F: Insulin	ECOD (1.6)
C [auth L]	C1-set	e3kr3L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
C [auth L]	V-set	e3kr3L1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth D]	1.10.100.10	Mainly Alpha	Orthogonal Bundle	Insulin-like, subunit E	Insulin-like	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]	DX-2647 mAb, anti-IGF-II	VH-CH1	Homo sapiens (human)	IGHV3-2301, IGHJ302, IGHG101, IGHG102, IGHG1*04	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
C [auth L]	DX-2647 mAb, anti-IGF-II	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV3	-	insulin-like growth factor ii	SAbDab (2024-04-19)
C [auth L]	Light Chain	IGKV1	Kappa	insulin-like growth factor ii	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D]	PF00049	Insulin/IGF/Relaxin family (Insulin)	Insulin/IGF/Relaxin family	Superfamily includes insulins; relaxins; insulin-like growth factor; and bombyxin. All are secreted regulatory hormones. Disulfide rich, all-alpha fold. Alignment includes B chain, linker (which is processed out of the final product), and A chain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth H]	antibody-Fab (heavy chain)	-	-	-
A [auth D]	Insulin-like growth factor II	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity growth factor activity insulin receptor binding protein tyrosine kinase activator activity enzyme regulator activity transmembrane receptor protein tyrosine kinase activator activity protein kinase regulator activity protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity growth factor activity insulin receptor binding protein tyrosine kinase activator activity enzyme regulator activity transmembrane receptor protein tyrosine kinase activator activity protein kinase regulator activity kinase activator activity enzyme activator activity protein kinase activator activity kinase regulator activity cell adhesion molecule binding protein-containing complex binding integrin binding hormone activity protein serine/threonine kinase activator activity insulin-like growth factor receptor binding	developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation cell population proliferation placenta development developmental growth chordate embryonic development animal organ development growth tissue development developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation cell population proliferation placenta development developmental growth chordate embryonic development animal organ development growth tissue development embryo development in utero embryonic development cell proliferation involved in embryonic placenta development multicellular organism development embryonic placenta development spongiotrophoblast layer developmental growth embryo development ending in birth or egg hatching anatomical structure development spongiotrophoblast layer development spongiotrophoblast cell proliferation embryonic organ development regulation of muscle tissue development regulation of growth regulation of developmental process skeletal muscle tissue development positive regulation of skeletal muscle tissue development positive regulation of biological process regulation of skeletal muscle tissue development muscle structure development positive regulation of developmental process skeletal muscle organ development regulation of skeletal muscle tissue growth positive regulation of skeletal muscle tissue growth muscle tissue development muscle organ development positive regulation of developmental growth regulation of biological process regulation of developmental growth biological regulation positive regulation of growth positive regulation of muscle tissue development skeletal muscle tissue growth anatomical structure morphogenesis animal organ morphogenesis regulation of cellular process regulation of generation of precursor metabolites and energy positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of glycogen metabolic process positive regulation of metabolic process regulation of small molecule metabolic process organic substance biosynthetic process small molecule metabolic process positive regulation of macromolecule metabolic process carbohydrate biosynthetic process cellular metabolic process primary metabolic process regulation of cellular metabolic process hexose metabolic process positive regulation of glucose metabolic process positive regulation of glycogen biosynthetic process biosynthetic process metabolic process energy reserve metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of carbohydrate metabolic process regulation of glycogen metabolic process regulation of metabolic process monosaccharide metabolic process regulation of glycogen biosynthetic process glucan biosynthetic process energy derivation by oxidation of organic compounds cellular biosynthetic process regulation of glucan biosynthetic process positive regulation of cellular metabolic process regulation of polysaccharide metabolic process polysaccharide metabolic process organic substance metabolic process glucan metabolic process positive regulation of biosynthetic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process regulation of biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process glycogen metabolic process generation of precursor metabolites and energy regulation of macromolecule metabolic process glycogen biosynthetic process macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of polysaccharide biosynthetic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process positive regulation of cellular biosynthetic process glucose metabolic process negative regulation of developmental process negative regulation of biological process negative regulation of muscle cell differentiation regulation of cell differentiation muscle cell differentiation regulation of muscle cell differentiation negative regulation of cellular process negative regulation of cell differentiation cellular response to stimulus positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction response to stimulus signaling regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling cell surface receptor signaling pathway insulin-like growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway positive regulation of cell division cell division regulation of cell division positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization regulation of mitotic nuclear division positive regulation of mitotic nuclear division mitotic cell cycle cellular component organization regulation of mitotic cell cycle positive regulation of cell cycle process cellular component organization or biogenesis cell cycle regulation of cell cycle cell cycle process mitotic nuclear division regulation of cell cycle process organelle fission positive regulation of nuclear division regulation of organelle organization positive regulation of cell cycle organelle organization nuclear division mitotic cell cycle process regulation of nuclear division positive regulation of cell population proliferation regulation of cell population proliferation digestive system development gland development exocrine pancreas development pancreas development exocrine system development system development cellular response to nitrogen compound response to organic substance response to peptide hormone insulin receptor signaling pathway regulation of cellular response to insulin stimulus cellular response to endogenous stimulus response to hormone cellular response to organic substance cellular response to hormone stimulus positive regulation of cellular response to insulin stimulus response to endogenous stimulus response to organonitrogen compound regulation of insulin receptor signaling pathway positive regulation of insulin receptor signaling pathway response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to organonitrogen compound response to chemical response to insulin cellular response to insulin stimulus 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 positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of activated T cell 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 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 T cell proliferation regulation of lymphocyte proliferation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of T cell proliferation immune system process regulation of mononuclear cell proliferation regulation of lymphocyte activation positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process gene expression nucleic acid metabolic process organic cyclic compound metabolic process regulation of gene expression organic cyclic compound biosynthetic process regulation of DNA-templated transcription endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of vascular endothelial cell proliferation regulation of endothelial cell proliferation positive regulation of endothelial cell proliferation vascular endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation positive regulation of vascular endothelial cell proliferation positive regulation of organ growth organ growth regulation of organ growth regulation of multicellular organism growth positive regulation of multicellular organism growth multicellular organism growth embryonic morphogenesis embryonic placenta morphogenesis striated muscle cell differentiation sexual reproduction reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation protein-DNA complex organization chromatin organization chromatin remodeling epigenetic programming of gene expression protein-containing complex organization epigenetic regulation of gene expression multicellular organismal reproductive process genomic imprinting germ cell development negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of RNA biosynthetic process regulation of protein modification process positive regulation of phosphorylation regulation of protein phosphorylation positive regulation of protein metabolic process peptidyl-tyrosine modification positive regulation of phosphate metabolic process positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process positive regulation of protein phosphorylation organonitrogen compound metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process regulation of peptidyl-tyrosine phosphorylation macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process peptidyl-tyrosine phosphorylation	extracellular region cellular anatomical entity membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle extracellular region cellular anatomical entity membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen organelle secretory granule secretory vesicle cytoplasm platelet alpha granule vesicle platelet alpha granule lumen extracellular space
C [auth L]	antibody-Fab (light chain)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D]	IPR022352	Insulin family	Family
A [auth D]	IPR016179	Insulin-like	Domain
A [auth D]	IPR013576	Insulin-like growth factor II E-peptide, C-terminal	Domain
A [auth D]	IPR022350	Insulin-like growth factor	Family
A [auth D]	IPR022334	Insulin-like growth factor II	Family
A [auth D]	IPR022353	Insulin, conserved site	Conserved Site
A [auth D]	IPR036438	Insulin-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth D]	Pharos: P01344	Beckwith-Wiedemann syndrome Silver-Russell syndrome kidney Wilms tumor Silver-Russell syndrome 3 adrenal cortex carcinoma rhabdomyosarcoma Alzheimer disease hepatoblastoma Bone Diseases, Developmental liver cancer colorectal cancer placenta disease Lewy body dementia malignant colon neoplasm Parkinson disease Beckwith-Wiedemann syndrome Silver-Russell syndrome kidney Wilms tumor Silver-Russell syndrome 3 adrenal cortex carcinoma rhabdomyosarcoma Alzheimer disease hepatoblastoma Bone Diseases, Developmental liver cancer colorectal cancer placenta disease Lewy body dementia malignant colon neoplasm Parkinson disease anemia atherosclerosis obesity disorder hypoglycemia isolated hemihyperplasia polyhydramnios large cell medulloblastoma prostate carcinoma cervical cancer lung cancer malignant mesothelioma common variable immunodeficiency type 1 diabetes mellitus adrenal carcinoma Duchenne muscular dystrophy ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia genetic endocrine growth disease Pick disease hepatocellular carcinoma intellectual disability juvenile dermatomyositis precancerous condition benign colon neoplasm breast carcinoma psoriasis rigid spine muscular dystrophy 1 colorectal carcinoma medulloblastoma Wilms tumor 1 cystic fibrosis Emery-Dreifuss muscular dystrophy pancreatic intraductal papillary-mucinous carcinoma fetal growth restriction pilocytic astrocytoma hereditary Wilms tumor invasive ductal breast carcinoma Becker muscular dystrophy limb-girdle muscular dystrophy prostate cancer cancer liver neoplasm colonic neoplasm malignant ependymoma schizophrenia congenital diaphragmatic hernia pancreatic intraductal papillary-mucinous neoplasm Perlman syndrome arteriosclerosis disorder pituitary cancer autism

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.