3QD6 | pdb_00003qd6

Crystal structure of the CD40 and CD154 (CD40L) complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	TNF-like	8041217	3000061	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TNF-like	8041217	3000061	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TNF-like	8041217	3000061	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	TNF-like	8041217	3000061	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	TNF-like	8041217	3000061	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TNF-like	8041217	3000061	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	Spectrin	e3qd6A1	A: alpha bundles	X: N-terminal beta-sandwich domain in anthrax protective antigen	H: Macro domain-like	T: Macro domain-like	F: Spectrin	ECOD (develop294)
B	AAA	e3qd6B1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (develop294)
C	AAA	e3qd6C1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (develop294)
F	AAA	e3qd6F1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (develop294)
E	AAA	e3qd6E1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (develop294)
D	AAA	e3qd6D1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (develop294)
H [auth S]	AAA	e3qd6S1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (develop294)
J [auth U]	AAA	e3qd6U1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (develop294)
I [auth T]	AAA	e3qd6T1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (develop294)
G [auth R]	Ribosomal_L34	e3qd6R1	A: alpha bundles	X: Globin-like	H: Globin-like	T: Globin-like	F: Ribosomal_L34	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
F	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
E	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
H [auth S]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
J [auth U]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
I [auth T]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
G [auth R]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00229	TNF(Tumour Necrosis Factor) family (TNF)	TNF(Tumour Necrosis Factor) family		Domain
G [auth R], H [auth S], I [auth T], J [auth U]	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, B, C, D, E A, B, C, D, E, F	CD40 ligand	protein binding binding signaling receptor binding cytokine receptor binding tumor necrosis factor receptor superfamily binding CD40 receptor binding cell adhesion molecule binding protein-containing complex binding integrin binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity protein binding binding signaling receptor binding cytokine receptor binding tumor necrosis factor receptor superfamily binding CD40 receptor binding cell adhesion molecule binding protein-containing complex binding integrin binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity tumor necrosis factor receptor binding enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity	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 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 cellular process positive regulation of signaling developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development leukocyte differentiation negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death integrin-mediated signaling pathway cell surface receptor signaling pathway extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of programmed cell death positive regulation of extrinsic apoptotic signaling pathway positive regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of apoptotic signaling pathway regulation of interleukin-12 production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of multicellular organismal process interleukin-12 production regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of interleukin-12 production regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process 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 production of molecular mediator of immune response regulation of immune effector process immunoglobulin production immune effector process regulation of immunoglobulin production regulation of immune system process regulation of production of molecular mediator of immune response interleukin-10 production regulation of interleukin-10 production positive regulation of interleukin-10 production positive regulation of endothelial cell apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic process cell adhesion cell-cell adhesion leukocyte cell-cell adhesion regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation T cell activation positive regulation of leukocyte activation regulation of cell-cell adhesion positive regulation of immune system process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation lymphocyte costimulation regulation of leukocyte cell-cell adhesion T cell costimulation regulation of lymphocyte activation defense response inflammatory response immune system development adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity immunoglobulin production involved in immunoglobulin-mediated immune response somatic cell DNA recombination B cell activation involved in immune response cell activation involved in immune response nucleobase-containing compound metabolic process multicellular organism development somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments leukocyte activation involved in immune response leukocyte mediated immunity somatic diversification of immune receptors lymphocyte activation involved in immune response somatic recombination of immunoglobulin genes involved in immune response system development immune response DNA recombination primary metabolic process DNA metabolic process immunoglobulin mediated immune response adaptive immune response nucleic acid metabolic process somatic diversification of immunoglobulins somatic diversification of immune receptors via germline recombination within a single locus B cell mediated immunity isotype switching regulation of interleukin-4 production positive regulation of interleukin-4 production interleukin-4 production positive regulation of cell population proliferation regulation of leukocyte proliferation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation regulation of cell population proliferation positive regulation of leukocyte proliferation positive regulation of mononuclear cell proliferation T cell proliferation regulation of lymphocyte proliferation regulation of T cell proliferation regulation of mononuclear cell proliferation	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system extracellular region extracellular space
G [auth R], H [auth S], I [auth T], J [auth U]	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	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 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 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 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 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 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 regulation of B cell activation leukocyte activation involved in immune response 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 positive regulation of gene expression immune system process somatic diversification of immune receptors via germline recombination within a single locus cellular 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 regulation of adaptive immune response regulation of B cell mediated immunity somatic diversification of immunoglobulins 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 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 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 cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction signaling regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction 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 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 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 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 defense response to protozoan response to protozoan 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 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 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 inflammatory response positive regulation of cell population proliferation positive regulation of B cell proliferation regulation of B cell proliferation positive regulation of mononuclear cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation positive regulation of lymphocyte proliferation regulation of cell population proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation 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 defense response to virus response to virus positive regulation of DNA-templated transcription RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription 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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006052	Tumour necrosis factor domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR021184	Tumour necrosis factor, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR003263	CD40 ligand	Family
G [auth R], H [auth S], I [auth T], J [auth U]	IPR052135	Tumor Necrosis Factor Receptor Superfamily Member 5	Family
G [auth R], H [auth S], I [auth T], J [auth U]	IPR034021	Tumour necrosis factor receptor 5, N-terminal	Domain
G [auth R], H [auth S], I [auth T], J [auth U]	IPR001368	TNFR/NGFR cysteine-rich region	Domain
G [auth R], H [auth S], I [auth T], J [auth U]	IPR020435	Tumour necrosis factor receptor 5	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: P29965	hyper-IgM syndrome type 1 amyotrophic lateral sclerosis autoimmune disease allergic disease Chromosome Breakage coronary artery disease pulmonary hypertension pneumonia pneumonitis hyper-IgM syndrome X-linked acrogigantism due to Xq26 microduplication cancer hematologic disease lymphatic system disease
G [auth R], H [auth S], I [auth T], J [auth U]	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 endogenous depression 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 endogenous depression ulcerative colitis Graves disease Hodgkins lymphoma lymphatic system disease attention deficit hyperactivity disorder, inattentive type bipolar disorder osteosarcoma cancer cutaneous lupus erythematosus hematologic disease malignant mesothelioma autism spectrum disorder breast cancer pancreatic intraductal papillary-mucinous carcinoma diffuse large B-cell lymphoma systemic lupus erythematosus hepatitis B virus infection

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.