5DMJ

Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
B	d5dmjb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth E]	d5dmje_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth G]	d5dmjg_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	TNFR_c6	e5dmjA2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6	ECOD (1.6)
A	TNFRSF5	e5dmjA3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF5	ECOD (1.6)
A	TNFRSF11A_2nd	e5dmjA1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF11A_2nd	ECOD (1.6)
C [auth D]	TNFR_c6	e5dmjD1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6	ECOD (1.6)
C [auth D]	TNFRSF14	e5dmjD3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF14	ECOD (1.6)
C [auth D]	TNFR_c6_2,TNFRSF5	e5dmjD2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6_2,TNFRSF5	ECOD (1.6)
E [auth F]	TNFR_c6	e5dmjF3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6	ECOD (1.6)
E [auth F]	TNFRSF5	e5dmjF2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF5	ECOD (1.6)
E [auth F]	TNFRSF11A_2nd	e5dmjF1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF11A_2nd	ECOD (1.6)
B	V-set_12	e5dmjB1	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)
D [auth E]	V-set_12	e5dmjE1	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)
F [auth G]	V-set_12	e5dmjG1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
C [auth D]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
E [auth F]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth G]	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
A, C [auth D], E [auth F]	CD40	4TNFR-CYS	Homo sapiens (human)	CD40*01	R-LIKE-DOMAIN TNFR-CYS	RPI	4-TNFR-CYS	IMGT (202415-0)
B, D [auth E], F [auth G]	3H56-5 dAb	VH	Homo sapiens (human)	IGHV3-2301, IGHV3-23D01, IGHJ401, IGHJ501, IGHJ502, IGHJ402, IGHJ4*03	V-DOMAIN VH	IG	(VH)	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D [auth E], F [auth G]	Heavy Chain	IGHV3	-	tumor necrosis factor receptor superfamily member 5	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth D], E [auth F]	PF00020	TNFR/NGFR cysteine-rich region (TNFR_c6)	TNFR/NGFR cysteine-rich region	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth D], E [auth F]	Tumor necrosis factor receptor superfamily member 5	ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding protein domain specific binding molecular transducer activity signaling receptor activity antigen binding	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 organic substance biosynthetic process regulation of immune system process positive regulation of macromolecule metabolic process system development positive regulation of DNA recombination 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 organic substance biosynthetic process 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 cellular metabolic process 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 positive regulation of cellular metabolic process 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 leukocyte activation involved in immune response regulation of B cell activation 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 regulation of cellular biosynthetic process positive regulation of gene expression immune system process somatic diversification of immune receptors via germline recombination within a single locus cellular process positive regulation of cellular biosynthetic 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 positive regulation of nucleobase-containing compound metabolic process regulation of adaptive immune response regulation of cellular metabolic process regulation of B cell mediated immunity somatic diversification of immunoglobulins organic cyclic compound metabolic process 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 cellular biosynthetic process 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 organic substance metabolic process 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 response to peptide response to organic substance response to chemical cellular response to stimulus response to cytokine response to erythropoietin cellular response to chemical stimulus cellular response to erythropoietin cellular response to cytokine stimulus cellular response to organic substance inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis response to nutrient levels response to organonitrogen compound response to nutrient response to oxygen-containing compound response to nitrogen compound response to vitamin response to cobalamin response to organic cyclic compound cell surface receptor signaling pathway signaling cell communication CD40 signaling pathway signal transduction regulation of body fluid levels wound healing hemostasis blood coagulation response to stress coagulation regulation of biological quality response to wounding platelet activation biological process involved in interspecies interaction between organisms response to other organism defense response response to type II interferon defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism innate immune response response to external biotic stimulus defense response to protozoan response to protozoan positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity RNA metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process regulation of molecular function regulation of DNA-binding transcription factor activity organic cyclic compound biosynthetic process regulation of DNA-templated transcription 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 defense response to virus response to virus transcription by RNA polymerase II regulation of transcription by RNA polymerase II 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 cellular response to interleukin-1 response to interleukin-1 cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction regulation of signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling phosphatidylinositol 3-kinase/protein kinase B signal transduction protein kinase C signaling regulation of protein kinase C signaling positive regulation of protein kinase C signaling positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity response to lipid cellular response to lipopolysaccharide cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to biotic stimulus response to bacterium cellular response to lipid response to molecule of bacterial origin regulation of interleukin-12 production cytokine production regulation of cytokine production interleukin-12 production positive regulation of interleukin-12 production positive regulation of cytokine production regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus pattern recognition receptor signaling pathway regulation of response to external stimulus toll-like receptor signaling pathway immune response-activating signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress innate immune response-activating signaling pathway positive regulation of innate immune response regulation of innate immune response TRIF-dependent toll-like receptor signaling pathway positive regulation of defense response activation of innate immune response MyD88-independent toll-like receptor signaling pathway activation of immune response cellular response to tumor necrosis factor response to tumor necrosis factor positive regulation of locomotion regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration positive regulation of cell migration positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration positive regulation of cell motility regulation of cell migration blood vessel endothelial cell migration regulation of endothelial cell migration epithelial cell migration cell migration cell motility regulation of epithelial cell migration locomotion positive regulation of blood vessel endothelial cell migration epithelium migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of phosphorylation regulation of transferase activity positive regulation of phosphate metabolic process regulation of MAP kinase activity positive regulation of protein serine/threonine kinase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process protein modification process positive regulation of protein phosphorylation positive regulation of MAP kinase activity protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation positive regulation of MAPK cascade regulation of protein metabolic process regulation of MAPK cascade positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity macromolecule modification regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of protein modification process protein metabolic process positive regulation of protein kinase activity organonitrogen compound metabolic process positive regulation of transferase activity regulation of protein kinase activity MAPK cascade regulation of phosphorylation 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 angiogenesis regulation of vasculature development tube morphogenesis regulation of anatomical structure morphogenesis blood vessel development regulation of multicellular organismal development blood vessel morphogenesis tube development positive regulation of angiogenesis vasculature development circulatory system development anatomical structure morphogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis peptidyl-amino acid modification tyrosine phosphorylation of STAT protein cell surface receptor signaling pathway via STAT peptidyl-tyrosine modification 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 peptidyl-tyrosine phosphorylation cell surface receptor signaling pathway via JAK-STAT positive regulation of epithelial cell apoptotic process positive regulation of endothelial cell apoptotic process positive regulation of programmed cell death regulation of epithelial cell apoptotic process regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process epithelial cell apoptotic process endothelial cell apoptotic process apoptotic process programmed cell death regulation of endothelial cell apoptotic process immune response-regulating cell surface receptor signaling pathway inflammatory response	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex CD40 receptor complex receptor complex extracellular exosome cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex CD40 receptor complex receptor complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle somatodendritic compartment cell body neuronal cell body axon cell projection main axon neuron projection varicosity plasma membrane bounded cell projection intracellular organelle intracellular anatomical structure intracellular membrane-bounded organelle
B, D [auth E], F [auth G]	3H65-5 domain antibody (dAb)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth D], E [auth F]	IPR034021	Tumour necrosis factor receptor 5, N-terminal	Domain
A, C [auth D], E [auth F]	IPR020435	Tumour necrosis factor receptor 5	Family
A, C [auth D], E [auth F]	IPR001368	TNFR/NGFR cysteine-rich region	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth D], E [auth F]	Pharos: P25942	rheumatoid arthritis mucocutaneous lymph node syndrome status epilepticus hyper-IgM syndrome type 1 breast carcinoma Crohn disease hyper-IgM syndrome type 3 multiple sclerosis hyper-IgM syndrome inflammatory bowel disease Hyper-IgM Immunodeficiency Syndrome, Type 3 lung cancer arthritic joint disease autoimmune disease ulcerative colitis rheumatoid arthritis mucocutaneous lymph node syndrome status epilepticus hyper-IgM syndrome type 1 breast carcinoma Crohn disease hyper-IgM syndrome type 3 multiple sclerosis hyper-IgM syndrome inflammatory bowel disease Hyper-IgM Immunodeficiency Syndrome, Type 3 lung cancer arthritic joint disease autoimmune disease ulcerative colitis endogenous depression Graves disease Hodgkins lymphoma lymphatic system disease attention deficit hyperactivity disorder, inattentive type osteosarcoma bipolar disorder cancer cutaneous lupus erythematosus hematologic disease malignant mesothelioma autism spectrum disorder pancreatic intraductal papillary-mucinous carcinoma breast cancer systemic lupus erythematosus diffuse large B-cell lymphoma hepatitis B virus infection

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.