Annotations: 8YX9

CD40 in complex with Dacetuzumab Fab

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth H]	Lip_C	e8yx9H01	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Lip_C	ECOD (v295)
G		e8yx9G1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
E		e8yx9E1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
C [auth B]		e8yx9B1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
B [auth L]	Lip_C	e8yx9L01	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Lip_C	ECOD (v295)
D [auth C]		e8yx9C1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
F		e8yx9F1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
H [auth I]		e8yx9I1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
I [auth A]		e8yx9A1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
J [auth D]		e8yx9D1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
L [auth K]		e8yx9K1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
K [auth J]		e8yx9J1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H], C [auth B], E, G	Heavy Chain	IGHV3	-	tumor necrosis factor receptor superfamily member 5	SAbDab (2026-06-26)
B [auth L], D [auth C], F, H [auth I]	Light Chain	IGKV1	Kappa	tumor necrosis factor receptor superfamily member 5	SAbDab (2026-06-26)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A [auth H], C [auth B], E, G	Dacetuzumab	TNFRSF5/CD40	Therapeutic SAbDab (2026-06-26)
B [auth L], D [auth C], F, H [auth I]	Cifurtilimab	TNFRSF5/CD40	Therapeutic SAbDab (2026-06-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth A], J [auth D], K [auth J], L [auth K]	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 [auth H], C [auth B], E, G	Dacetuzumab, Heavy chain	-	-	-
B [auth L], D [auth C], F, H [auth I]	Dacetuzumab, light chain	-	-	-
I [auth A], J [auth D], K [auth J], L [auth K]	Tumor necrosis factor receptor superfamily member 5	protein binding binding protein domain specific binding molecular transducer activity signaling receptor activity antigen binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process 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 positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling protein kinase C signaling regulation of protein kinase C signaling positive regulation of protein kinase C signaling adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity immune response immune system process B cell mediated immunity leukocyte mediated immunity adaptive immune response immune effector process multicellular organismal process B cell activation cell activation lymphocyte activation leukocyte activation response to peptide cellular response to erythropoietin response to chemical response to cytokine cellular response to cytokine stimulus response to erythropoietin biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin 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 cobalamin response to nutrient response to nitrogen compound response to vitamin cell surface receptor signaling pathway CD40 signaling pathway regulation of body fluid levels wound healing hemostasis blood coagulation response to stress coagulation regulation of biological quality response to wounding platelet activation cell population proliferation B cell proliferation leukocyte proliferation mononuclear cell proliferation lymphocyte proliferation defense response response to type II interferon defense response to symbiont defense response to other organism innate immune response cellular response to tumor necrosis factor response to tumor necrosis factor cell surface receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT 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 blood vessel endothelial cell migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of cell motility regulation of cell migration blood vessel endothelial cell migration regulation of endothelial cell migration cell migration cell motility locomotion positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade 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 regulation of developmental process angiogenesis regulation of vasculature development positive regulation of developmental process multicellular organism development tube morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development developmental process 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 positive regulation of multicellular organismal process animal gross anatomical part developmental process positive regulation of endothelial cell apoptotic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of 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 immune response-regulating signaling pathway regulation of immune response regulation of immune system process inflammatory response positive regulation of response to cytokine stimulus cytokine-mediated signaling pathway response to interleukin-4 cellular response to interleukin-4 positive regulation of interleukin-4-mediated signaling pathway interleukin-4-mediated signaling pathway regulation of cytokine-mediated signaling pathway regulation of interleukin-4-mediated signaling pathway regulation of response to cytokine stimulus positive regulation of cytokine-mediated signaling pathway positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process cellular response to interleukin-1 response to interleukin-1	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane axon cell projection main axon neuron projection varicosity plasma membrane bounded cell projection protein-containing complex cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane axon cell projection main axon neuron projection varicosity plasma membrane bounded cell projection protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex signaling receptor complex CD40 receptor complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle somatodendritic compartment cell body neuronal cell body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth A], J [auth D], K [auth J], L [auth K]	IPR052135	Tumor Necrosis Factor Receptor Superfamily Member 5	Family
I [auth A], J [auth D], K [auth J], L [auth K]	IPR034021	Tumour necrosis factor receptor 5, N-terminal	Domain
I [auth A], J [auth D], K [auth J], L [auth K]	IPR001368	TNFR/NGFR cysteine-rich region	Domain
I [auth A], J [auth D], K [auth J], L [auth K]	IPR020435	Tumour necrosis factor receptor 5	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
I [auth A], J [auth D], K [auth J], L [auth K]	: 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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.