5YGP | pdb_00005ygp

Human TNFRSF25 death domain mutant-D412E

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	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DEATH domain	8095579	3000069	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DEATH domain	8095579	3000069	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DEATH domain	8095579	3000069	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DEATH domain	8095579	3000069	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	Death	e5ygpA1	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: Death	ECOD (1.6)
A	SBP_bac_1_C	e5ygpA3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
A	SBP_bac_1_C,SBP_bac_1_N_2	e5ygpA4	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C,SBP_bac_1_N_2	ECOD (1.6)
B	Death	e5ygpB3	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: Death	ECOD (1.6)
B	SBP_bac_1_C	e5ygpB2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
B	SBP_bac_1_C,SBP_bac_1_N_2	e5ygpB4	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C,SBP_bac_1_N_2	ECOD (1.6)
C	Death	e5ygpC1	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: Death	ECOD (1.6)
C	SBP_bac_1_C	e5ygpC2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
C	SBP_bac_1_C,SBP_bac_1_N_2	e5ygpC3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C,SBP_bac_1_N_2	ECOD (1.6)
D	Death	e5ygpD3	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: Death	ECOD (1.6)
D	SBP_bac_1_C	e5ygpD1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
D	SBP_bac_1_C,SBP_bac_1_N_2	e5ygpD4	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C,SBP_bac_1_N_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
C	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
D	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01547	Bacterial extracellular solute-binding protein (SBP_bac_1)	Bacterial extracellular solute-binding protein	-	Family
A, B, C, D	PF00531	Death domain (Death)	Death domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	TNFRSF25 death domain	transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding molecular transducer activity signaling receptor activity transmembrane signaling receptor activity tumor necrosis factor receptor activity death receptor activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility locomotion localization transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport response to disaccharide response to oxygen-containing compound detection of maltose stimulus detection of stimulus response to carbohydrate detection of chemical stimulus detection of disaccharide stimulus response to maltose detection of carbohydrate stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling biological regulation signal transduction cell communication cell death apoptotic signaling pathway apoptotic process programmed cell death regulation of apoptotic process regulation of programmed cell death	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space outer membrane-bounded periplasmic space cell envelope extracellular region intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR006061	Solute-binding family 1, conserved site	Conserved Site
A, B, C, D	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
A, B, C, D	IPR006059	Bacterial-type extracellular solute-binding protein	Family
A, B, C, D	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR022329	Tumour necrosis factor receptor 25	Family
A, B, C, D	IPR000488	Death domain	Domain
A, B, C, D	IPR001368	TNFR/NGFR cysteine-rich region	Domain
A, B, C, D	IPR034050	Tumor necrosis factor receptor 25, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q93038	autoimmune disease DOID:0081062 large cell medulloblastoma malignant glioma Pick disease tuberculosis breast carcinoma glioblastoma lung adenocarcinoma osteosarcoma pilocytic astrocytoma cutaneous lupus erythematosus inborn carbohydrate metabolic disorder lung cancer pancreatic ductal adenocarcinoma autoimmune disease DOID:0081062 large cell medulloblastoma malignant glioma Pick disease tuberculosis breast carcinoma glioblastoma lung adenocarcinoma osteosarcoma pilocytic astrocytoma cutaneous lupus erythematosus inborn carbohydrate metabolic disorder lung cancer pancreatic ductal adenocarcinoma psoriasis

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.