4N90 | pdb_00004n90

Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
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)
D [auth A]	SCOP2B Superfamily	TNF-like	8041237	3000061	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	TNF-like	8041237	3000061	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	TNF-like	8041237	3000061	SCOP2B (2022-06-29)
A [auth R]	SCOP2B Superfamily	TNF receptor-like	8038905	3000971	SCOP2B (2022-06-29)
A [auth R]	SCOP2B Superfamily	TNF receptor-like	8038907	3000971	SCOP2B (2022-06-29)
A [auth R]	SCOP2B Superfamily	TNF receptor-like	8038908	3000971	SCOP2B (2022-06-29)
C [auth T]	SCOP2B Superfamily	TNF receptor-like	8038905	3000971	SCOP2B (2022-06-29)
C [auth T]	SCOP2B Superfamily	TNF receptor-like	8038908	3000971	SCOP2B (2022-06-29)
C [auth T]	SCOP2B Superfamily	TNF receptor-like	8038907	3000971	SCOP2B (2022-06-29)
B [auth S]	SCOP2B Superfamily	TNF receptor-like	8038907	3000971	SCOP2B (2022-06-29)
B [auth S]	SCOP2B Superfamily	TNF receptor-like	8038905	3000971	SCOP2B (2022-06-29)
B [auth S]	SCOP2B Superfamily	TNF receptor-like	8038908	3000971	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)
I [auth G]	V-set	e4n90G1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)
K [auth I]	V-set	e4n90I1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)
G [auth E]	V-set	e4n90E1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)
J [auth F]	V-set	e4n90F1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)
L [auth H]	V-set	e4n90H1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)
H [auth D]	V-set	e4n90D1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)
D [auth A]	V-set	e4n90A1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)
F [auth C]	V-set	e4n90C1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)
E [auth B]	V-set	e4n90B1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)
A [auth R]	V-set	e4n90R1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)
C [auth T]	V-set	e4n90T1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)
B [auth S]	V-set	e4n90S1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ribosomal protein L41-A	T: Ribosomal protein L41-A	F: V-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I [auth G]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
L [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth A]	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
F [auth C]	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
E [auth B]	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
A [auth R]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
C [auth T]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
B [auth S]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	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
G [auth E], I [auth G], K [auth I]	DR5 Fab	L-KAPPA	Homo sapiens (human)	IGKV3-2001, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202613-0)
H [auth D], J [auth F], L [auth H]	DR5 Fab	VH-CH1	Homo sapiens (human)	IGHV4-30-401, IGHJ601, IGHJ602, IGHG101, IGHG102, IGHG104	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202613-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G [auth E], I [auth G], K [auth I]	Light Chain	IGKV3	Kappa	tumor necrosis factor receptor superfamily member 10b \| tumor necrosis factor ligand superfamily member 10	SAbDab (2026-04-10)
H [auth D], J [auth F], L [auth H]	Heavy Chain	IGHV4	-	tumor necrosis factor receptor superfamily member 10b \| tumor necrosis factor ligand superfamily member 10	SAbDab (2026-04-10)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
G [auth E], I [auth G], K [auth I]	Conatumumab	TNFRSF10B/CD262/DR5/TRAILR2	Therapeutic SAbDab (2026-04-10)
H [auth D], J [auth F], L [auth H]	Conatumumab	TNFRSF10B/CD262/DR5/TRAILR2	Therapeutic SAbDab (2026-04-10)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth A], E [auth B], F [auth C]	PF00229	TNF(Tumour Necrosis Factor) family (TNF)	TNF(Tumour Necrosis Factor) family		Domain
A [auth R], B [auth S], C [auth T]	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
G [auth E], I [auth G], K [auth I]	Fab light chain	-	-	-
H [auth D], J [auth F], L [auth H]	Fab heavy chain	-	-	-
D [auth A], E [auth B], F [auth C]	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	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 cell surface receptor signaling pathway 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 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 positive regulation of extrinsic apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway regulation of apoptotic signaling pathway extrinsic apoptotic signaling pathway via death domain receptors TRAIL-activated apoptotic signaling pathway	cellular anatomical structure extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane
A [auth R], B [auth S], C [auth T]	Tumor necrosis factor receptor superfamily member 10B	molecular transducer activity signaling receptor activity protein binding binding TRAIL binding TRAIL receptor activity transmembrane signaling receptor activity death receptor activity	response to tumor cell response to stimulus defense response response to stress defense response to tumor cell response to biotic stimulus cellular response to stimulus regulation of cellular process positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process intracellular signal transduction regulation of primary metabolic process response to tumor cell response to stimulus defense response response to stress defense response to tumor cell response to biotic stimulus cellular response to stimulus regulation of cellular process positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process intracellular signal transduction regulation of primary metabolic process cell communication positive regulation of metabolic process phosphate-containing compound metabolic process intracellular signaling cassette 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 regulation of protein 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 regulation of protein phosphorylation signaling positive regulation of protein metabolic process positive regulation of biological process positive regulation of molecular function positive regulation of protein modification process protein metabolic process positive regulation of protein kinase activity positive regulation of cellular process biological regulation positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of phosphorylation cellular process positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction regulation of signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signaling 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 cell surface receptor signaling pathway 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 intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress cell death apoptotic signaling pathway cellular response to stress apoptotic process intrinsic apoptotic signaling pathway programmed cell death response to endoplasmic reticulum stress positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process extrinsic apoptotic signaling pathway via death domain receptors extrinsic apoptotic signaling pathway TRAIL-activated apoptotic signaling pathway	cell surface cellular anatomical structure cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth A], E [auth B], F [auth C]	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
D [auth A], E [auth B], F [auth C]	IPR006052	Tumour necrosis factor domain	Domain
D [auth A], E [auth B], F [auth C]	IPR021184	Tumour necrosis factor, conserved site	Conserved Site
D [auth A], E [auth B], F [auth C]	IPR017355	Tumour necrosis factor ligand 10/11	Family
A [auth R], B [auth S], C [auth T]	IPR011029	Death-like domain superfamily	Homologous Superfamily
A [auth R], B [auth S], C [auth T]	IPR020465	Tumour necrosis factor receptor 10	Family
A [auth R], B [auth S], C [auth T]	IPR052491	Tumor necrosis factor receptor superfamily member 10	Family
A [auth R], B [auth S], C [auth T]	IPR000488	Death domain	Domain
A [auth R], B [auth S], C [auth T]	IPR001368	TNFR/NGFR cysteine-rich region	Domain
A [auth R], B [auth S], C [auth T]	IPR034029	Tumour necrosis factor receptor 10A/B, death domain	Domain
A [auth R], B [auth S], C [auth T]	IPR034024	Tumor necrosis factor receptor 10, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth A], E [auth B], F [auth C]	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 pituitary cancer clear cell renal carcinoma lung carcinoma renal carcinoma cystic fibrosis ulcerative colitis estrogen-receptor negative breast cancer adenoma oligodendroglioma atypical teratoid rhabdoid tumor pancreatic ductal adenocarcinoma kidney cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast cancer lung adenocarcinoma plasma cell myeloma colorectal carcinoma malignant mesothelioma Crohn disease MALT lymphoma subependymal giant cell astrocytoma Duchenne muscular dystrophy multiple sclerosis Gaucher disease adrenal cortex carcinoma glioma benign colon neoplasm pancreatic intraductal papillary-mucinous carcinoma brain injury kidney neoplasm pancreatic neoplasm pilocytic astrocytoma chronic obstructive pulmonary disease lung cancer primitive neuroectodermal tumor colonic neoplasm malignant ependymoma psoriasis cutaneous lupus erythematosus tuberculosis endometrial cancer medulloblastoma endometriosis atopic eczema ovarian neoplasm juvenile dermatomyositis pancreatic intraductal papillary-mucinous neoplasm cancer liver neoplasm
A [auth R], B [auth S], C [auth T]	Pharos: O14763	head and neck squamous cell carcinoma Liver Neoplasms, Experimental malignant colon neoplasm malignant mesothelioma myopathy osteosarcoma acute myeloid leukemia pancreatic intraductal papillary-mucinous neoplasm B-cell chronic lymphocytic leukemia pituitary cancer cutaneous lupus erythematosus renal cell carcinoma squamous cell carcinoma of lip subependymal giant cell astrocytoma juvenile dermatomyositis head and neck squamous cell carcinoma Liver Neoplasms, Experimental malignant colon neoplasm malignant mesothelioma myopathy osteosarcoma acute myeloid leukemia pancreatic intraductal papillary-mucinous neoplasm B-cell chronic lymphocytic leukemia pituitary cancer cutaneous lupus erythematosus renal cell carcinoma squamous cell carcinoma of lip subependymal giant cell astrocytoma juvenile dermatomyositis lung cancer malignant ependymoma oligodendroglioma ovarian cancer astrocytic tumor pancreatic neoplasm Barrett esophagus polycystic ovary syndrome dermatomyositis skin basal cell carcinoma gastric carcinoma ulcerative colitis laryngeal squamous cell carcinoma lung carcinoma malignant glioma malignant pancreatic neoplasm oral cavity squamous cell carcinoma pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor pilocytic astrocytoma cancer primitive neuroectodermal tumor esophageal adenocarcinoma glioblastoma

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.