5CIR

Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10)

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5cira_	All beta proteins	TNF-like	TNF-like	TNF-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5cirb_	All beta proteins	TNF-like	TNF-like	TNF-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth D]	d5cird_	All beta proteins	TNF-like	TNF-like	TNF-like	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	SCOP2B Superfamily	TNF-like	8041237	3000061	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TNF-like	8041237	3000061	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	TNF-like	8041237	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	TNF	e5cirA1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
B	TNF	e5cirB1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
C [auth D]	TNF	e5cirD1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
D [auth E]	TNFR_c6_1	e5cirE2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6_1	ECOD (1.6)
D [auth E]	TNFRSF10	e5cirE3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF10	ECOD (1.6)
D [auth E]	UNK_F_TYPE	e5cirE1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: UNK_F_TYPE	ECOD (1.6)
E [auth F]	TNFR_c6_1	e5cirF1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6_1	ECOD (1.6)
E [auth F]	TNFRSF10	e5cirF3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF10	ECOD (1.6)
E [auth F]	UNK_F_TYPE	e5cirF2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: UNK_F_TYPE	ECOD (1.6)
F [auth G]	TNFR_c6_1	e5cirG1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6_1	ECOD (1.6)
F [auth G]	TNFRSF10	e5cirG3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF10	ECOD (1.6)
F [auth G]	UNK_F_TYPE	e5cirG2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: UNK_F_TYPE	ECOD (1.6)

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 [auth D]	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D [auth E]	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)
F [auth G]	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 [auth D]	PF00229	TNF(Tumour Necrosis Factor) family (TNF)	TNF(Tumour Necrosis Factor) family	-	Domain
D [auth E], E [auth F], F [auth G]	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 [auth D]	Tumor necrosis factor ligand superfamily member 10	protein binding binding signaling receptor binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity TRAIL binding cation binding transition metal ion binding zinc ion binding ion binding protein binding binding signaling receptor binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity TRAIL binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding cytokine receptor binding tumor necrosis factor receptor superfamily binding tumor necrosis factor receptor binding identical protein binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development 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 immune response immune system process positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization apoptotic mitochondrial changes regulation of release of cytochrome c from mitochondria cellular component organization positive regulation of release of cytochrome c from mitochondria cellular component organization or biogenesis mitochondrion organization cell death regulation of organelle organization apoptotic signaling pathway release of cytochrome c from mitochondria organelle organization regulation of mitochondrion organization apoptotic process programmed cell death response to organic substance response to hormone response to chemical response to endogenous stimulus response to organonitrogen compound response to peptide hormone response to insulin response to oxygen-containing compound response to nitrogen compound positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process cell-cell signaling extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway cell surface receptor signaling pathway positive regulation of extrinsic apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway regulation of apoptotic signaling pathway regulation of catalytic activity positive regulation of protein metabolic process positive regulation of peptidase activity positive regulation of cysteine-type endopeptidase activity involved in apoptotic process regulation of primary metabolic process positive regulation of molecular function positive regulation of metabolic process regulation of cysteine-type endopeptidase activity involved in apoptotic process organic substance metabolic process regulation of proteolysis proteolysis regulation of endopeptidase activity positive regulation of macromolecule metabolic process protein metabolic process regulation of cysteine-type endopeptidase activity organonitrogen compound metabolic process regulation of protein metabolic process regulation of peptidase activity positive regulation of catalytic activity primary metabolic process regulation of macromolecule metabolic process regulation of molecular function positive regulation of hydrolase activity positive regulation of cysteine-type endopeptidase activity regulation of hydrolase activity positive regulation of endopeptidase activity positive regulation of proteolysis metabolic process macromolecule metabolic process regulation of metabolic process	extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane
D [auth E], E [auth F], F [auth G]	Tumor necrosis factor receptor superfamily member 10A	molecular transducer activity signaling receptor activity transmembrane signaling receptor activity death receptor activity protein binding binding TRAIL binding enzyme binding protease binding identical protein binding	cellular response to stimulus regulation of cellular process response to stimulus positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process intracellular signal transduction cell communication regulation of primary metabolic process positive regulation of metabolic process regulation of phosphate metabolic process intracellular signaling cassette phosphate-containing compound metabolic process cellular response to stimulus regulation of cellular process response to stimulus positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process intracellular signal transduction cell communication regulation of primary metabolic process positive regulation of metabolic process regulation of phosphate metabolic process intracellular signaling cassette phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process signal transduction phosphorus metabolic process protein modification process positive regulation of protein phosphorylation activation of NF-kappaB-inducing kinase activity regulation of biological process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation non-canonical NF-kappaB signal transduction cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity activation of protein kinase activity macromolecule modification regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process signaling regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of molecular function positive regulation of protein modification process organic substance metabolic process protein metabolic process positive regulation of protein kinase activity positive regulation of cellular process organonitrogen compound metabolic process positive regulation of transferase activity biological regulation positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process cellular process regulation of phosphorylation response to mechanical stimulus response to external 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 apoptotic process cell death programmed cell death positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process cell surface receptor signaling pathway extrinsic apoptotic signaling pathway apoptotic signaling pathway extrinsic apoptotic signaling pathway via death domain receptors TRAIL-activated apoptotic signaling pathway	membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle endomembrane system cell surface cytosol cell periphery plasma membrane membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle endomembrane system cell surface cytosol cell periphery plasma membrane membrane membrane microdomain membrane raft

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth D]	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
A, B, C [auth D]	IPR006052	Tumour necrosis factor domain	Domain
A, B, C [auth D]	IPR021184	Tumour necrosis factor, conserved site	Conserved Site
A, B, C [auth D]	IPR017355	Tumour necrosis factor ligand 10/11	Family
D [auth E], E [auth F], F [auth G]	IPR011029	Death-like domain superfamily	Homologous Superfamily
D [auth E], E [auth F], F [auth G]	IPR020465	Tumour necrosis factor receptor 10	Family
D [auth E], E [auth F], F [auth G]	IPR000488	Death domain	Domain
D [auth E], E [auth F], F [auth G]	IPR001368	TNFR/NGFR cysteine-rich region	Domain
D [auth E], E [auth F], F [auth G]	IPR034029	Tumour necrosis factor receptor 10A/B, death domain	Domain
D [auth E], E [auth F], F [auth G]	IPR034024	Tumor necrosis factor receptor 10, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C [auth D]	Pharos: P50591	malignant glioma glioblastoma malignant colon neoplasm renal cell carcinoma acute myeloid leukemia neuroblastoma prostate cancer colorectal cancer malignant pancreatic neoplasm Mammary Neoplasms, Experimental endometrial carcinoma mixed glioma influenza liver cancer chromophobe renal cell carcinoma malignant glioma glioblastoma malignant colon neoplasm renal cell carcinoma acute myeloid leukemia neuroblastoma prostate cancer colorectal cancer malignant pancreatic neoplasm Mammary Neoplasms, Experimental endometrial carcinoma mixed glioma influenza liver cancer chromophobe renal cell carcinoma collecting duct carcinoma ovarian cancer breast carcinoma sarcomatoid renal cell carcinoma giant cell glioblastoma hepatocellular carcinoma leukemia papillary renal cell carcinoma lung carcinoma pituitary cancer clear cell renal carcinoma renal carcinoma cystic fibrosis ulcerative colitis estrogen-receptor negative breast cancer adenoma oligodendroglioma atypical teratoid rhabdoid tumor kidney cancer pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast cancer lung adenocarcinoma plasma cell myeloma malignant mesothelioma colorectal carcinoma Crohn disease MALT lymphoma subependymal giant cell astrocytoma Duchenne muscular dystrophy multiple sclerosis Gaucher disease adrenal cortex carcinoma glioma benign colon neoplasm kidney neoplasm pancreatic intraductal papillary-mucinous carcinoma brain injury pancreatic neoplasm lung cancer pilocytic astrocytoma chronic obstructive pulmonary disease malignant ependymoma primitive neuroectodermal tumor colonic neoplasm psoriasis cutaneous lupus erythematosus tuberculosis endometrial cancer medulloblastoma endometriosis atopic eczema ovarian neoplasm juvenile dermatomyositis pancreatic intraductal papillary-mucinous neoplasm liver neoplasm cancer
D [auth E], E [auth F], F [auth G]	Pharos: O00220	age-related macular degeneration neutropenia thrombocytopenia cancer Fatigue granular cell carcinoma malignant colon neoplasm peripheral neuropathy tubular adenocarcinoma drug allergy adenocarcinoma prostate cancer esophageal cancer alopecia peripheral nervous system disease age-related macular degeneration neutropenia thrombocytopenia cancer Fatigue granular cell carcinoma malignant colon neoplasm peripheral neuropathy tubular adenocarcinoma drug allergy adenocarcinoma prostate cancer esophageal cancer alopecia peripheral nervous system disease anemia neoplasm of esophagus acute myeloid leukemia osteosarcoma pancreatic intraductal papillary-mucinous neoplasm benign colon neoplasm colonic neoplasm malignant pancreatic neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia androgenetic alopecia arthritic joint disease rheumatoid arthritis benign neoplasm ulcerative colitis cribriform carcinoma gastric carcinoma leukopenia pancreatic intraductal papillary-mucinous carcinoma autoimmune disease wet macular degeneration cribriform carcinoma of breast

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.