1ZA3

The crystal structure of the YSd1 Fab bound to DR5

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
A	d1za3a1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1za3a2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth L]	d1za3l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth L]	d1za3l2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth H]	d1za3h1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Camelid IG heavy chain variable domain, VHh	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth H]	d1za3h2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1za3b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Camelid IG heavy chain variable domain, VHh	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1za3b2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth R]	d1za3r2	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Death receptor-5 (dr5) fragment, middle domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth R]	d1za3r1	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Death receptor-5 (dr5) fragment, N- and C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth S]	d1za3s2	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Death receptor-5 (dr5) fragment, middle domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth S]	d1za3s1	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Death receptor-5 (dr5) fragment, N- and C-terminal domain	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)
C [auth R]	SCOP2B Superfamily	TNF receptor-like	8038905	3000971	SCOP2B (2022-06-29)
C [auth R]	SCOP2B Superfamily	TNF receptor-like	8038907	3000971	SCOP2B (2022-06-29)
F [auth S]	SCOP2B Superfamily	TNF receptor-like	8038908	3000971	SCOP2B (2022-06-29)
F [auth S]	SCOP2B Superfamily	TNF receptor-like	8038907	3000971	SCOP2B (2022-06-29)
F [auth S]	SCOP2B Superfamily	TNF receptor-like	8038905	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)
A	PF07654	e1za3A2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
A	PF07686	e1za3A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D [auth L]	PF07654	e1za3L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D [auth L]	PF07686	e1za3L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
E [auth H]	PF07654	e1za3H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
E [auth H]	PF07686	e1za3H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B	PF07654	e1za3B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B	PF07686	e1za3B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth R]	F_UNCLASSIFIED	e1za3R3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth R]	PF00020	e1za3R2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: PF00020	ECOD (1.6)
F [auth S]	F_UNCLASSIFIED	e1za3S1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: F_UNCLASSIFIED	ECOD (1.6)
F [auth S]	PF00020	e1za3S2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: PF00020	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth R]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
F [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
A, D [auth L]	YSD1	L-KAPPA	Homo sapiens (human)	IGKV1D-1301, IGKJ201, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)
B, E [auth H]	YSD1	VH-CH1	Homo sapiens (human)	IGHV3-2101, IGHV3-2102, IGHV3-2304, IGHV3-2104, IGHV3-2103, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, D [auth L]	Light Chain	IGKV1	Kappa	tumor necrosis factor receptor superfamily member 10b	SAbDab (2024-04-26)
B, E [auth H]	Heavy Chain	IGHV3	-	tumor necrosis factor receptor superfamily member 10b	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth R], F [auth S]	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, D [auth L]	Fab-YSd1 light chain	-	-	-
B, E [auth H]	Fab-YSd1 heavy chain	-	-	-
C [auth R], F [auth S]	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 cell communication 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 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 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 entity cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth R], F [auth S]	IPR011029	Death-like domain superfamily	Homologous Superfamily
C [auth R], F [auth S]	IPR020465	Tumour necrosis factor receptor 10	Family
C [auth R], F [auth S]	IPR000488	Death domain	Domain
C [auth R], F [auth S]	IPR001368	TNFR/NGFR cysteine-rich region	Domain
C [auth R], F [auth S]	IPR034029	Tumour necrosis factor receptor 10A/B, death domain	Domain
C [auth R], F [auth S]	IPR034024	Tumor necrosis factor receptor 10, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth R], F [auth S]	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 pituitary cancer B-cell chronic lymphocytic leukemia renal cell carcinoma cutaneous lupus erythematosus 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 pituitary cancer B-cell chronic lymphocytic leukemia renal cell carcinoma cutaneous lupus erythematosus squamous cell carcinoma of lip subependymal giant cell astrocytoma juvenile dermatomyositis lung cancer malignant ependymoma oligodendroglioma ovarian cancer astrocytic tumor pancreatic neoplasm polycystic ovary syndrome Barrett esophagus skin basal cell carcinoma dermatomyositis gastric carcinoma ulcerative colitis laryngeal squamous cell carcinoma lung carcinoma malignant glioma malignant pancreatic neoplasm oral cavity squamous cell carcinoma pancreatic ductal adenocarcinoma pilocytic astrocytoma atypical teratoid rhabdoid tumor primitive neuroectodermal tumor cancer esophageal adenocarcinoma glioblastoma

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.