1Z6T

Structure of the apoptotic protease-activating factor 1 bound to ADP

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)
B	SCOP2B Superfamily	DEATH domain	8037979	3000069	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DEATH domain	8037979	3000069	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DEATH domain	8037979	3000069	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DEATH domain	8037979	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)
B	KOG4658_like	e1z6tB5	A: alpha arrays	X: HTH	H: HTH	T: winged	F: KOG4658_like	ECOD (1.6)
B	CARD	e1z6tB3	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)
B	NB-ARC_2nd	e1z6tB4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: NB-ARC_2nd	ECOD (1.6)
B	EUF08240	e1z6tB2	A: alpha superhelices	X: Apoptotic protease-activating factor 1 (Apaf-1) helical domain (From Topology)	H: Apoptotic protease-activating factor 1 (Apaf-1) helical domain (From Topology)	T: Apoptotic protease-activating factor 1 (Apaf-1) helical domain	F: EUF08240	ECOD (1.6)
B	NB-ARC_1st	e1z6tB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NB-ARC_1st	ECOD (1.6)
C	KOG4658_like	e1z6tC7	A: alpha arrays	X: HTH	H: HTH	T: winged	F: KOG4658_like	ECOD (1.6)
C	CARD	e1z6tC6	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)
C	NB-ARC_2nd	e1z6tC4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: NB-ARC_2nd	ECOD (1.6)
C	EUF08240	e1z6tC2	A: alpha superhelices	X: Apoptotic protease-activating factor 1 (Apaf-1) helical domain (From Topology)	H: Apoptotic protease-activating factor 1 (Apaf-1) helical domain (From Topology)	T: Apoptotic protease-activating factor 1 (Apaf-1) helical domain	F: EUF08240	ECOD (1.6)
C	NB-ARC_1st	e1z6tC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NB-ARC_1st	ECOD (1.6)
D	KOG4658_like	e1z6tD5	A: alpha arrays	X: HTH	H: HTH	T: winged	F: KOG4658_like	ECOD (1.6)
D	CARD	e1z6tD3	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)
D	NB-ARC_2nd	e1z6tD4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: NB-ARC_2nd	ECOD (1.6)
D	EUF08240	e1z6tD2	A: alpha superhelices	X: Apoptotic protease-activating factor 1 (Apaf-1) helical domain (From Topology)	H: Apoptotic protease-activating factor 1 (Apaf-1) helical domain (From Topology)	T: Apoptotic protease-activating factor 1 (Apaf-1) helical domain	F: EUF08240	ECOD (1.6)
D	NB-ARC_1st	e1z6tD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NB-ARC_1st	ECOD (1.6)
A	KOG4658_like	e1z6tA5	A: alpha arrays	X: HTH	H: HTH	T: winged	F: KOG4658_like	ECOD (1.6)
A	CARD	e1z6tA3	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: CARD	ECOD (1.6)
A	NB-ARC_2nd	e1z6tA4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: NB-ARC_2nd	ECOD (1.6)
A	EUF08240	e1z6tA2	A: alpha superhelices	X: Apoptotic protease-activating factor 1 (Apaf-1) helical domain (From Topology)	H: Apoptotic protease-activating factor 1 (Apaf-1) helical domain (From Topology)	T: Apoptotic protease-activating factor 1 (Apaf-1) helical domain	F: EUF08240	ECOD (1.6)
A	NB-ARC_1st	e1z6tA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: NB-ARC_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.10.8.430	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B	1.25.40.370	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
C	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	1.10.8.430	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
C	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C	1.25.40.370	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
D	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	1.10.8.430	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
D	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D	1.25.40.370	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.10.8.430	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	1.25.40.370	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00931	NB-ARC domain (NB-ARC)	NB-ARC domain	-	Domain
A, B, C, D	PF21296	Apoptotic protease-activating factor 1-like, winged-helix domain (APAF-1-like_WHD)	Apoptotic protease-activating factor 1-like, winged-helix domain	This domain is found in Apoptotic protease-activating factor 1 from Mus musculus (APAF-1), responsible to ignite the downstream cascade of caspases in the mitochondrial pathway of apoptosis. This entry represents the winged-helix domain (WHD) [1-5].	Domain
A, B, C, D	PF17908	APAF-1 helical domain (APAF1_C)	APAF-1 helical domain	This domain represents the C-terminal alpha helical domain of the apoptotic Apaf-1 protein.	Domain
A, B, C, D	PF00619	Caspase recruitment domain (CARD)	Caspase recruitment domain	Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (Pfam:PF00531) domain-like fold .	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Apoptotic protease activating factor 1	protein binding binding heat shock protein binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding protein binding binding heat shock protein binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ADP binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity cysteine-type endopeptidase activator activity involved in apoptotic process molecular function regulator activity cysteine-type endopeptidase regulator activity involved in apoptotic process peptidase activator activity peptidase activator activity involved in apoptotic process identical protein binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction regulation of programmed cell death positive regulation of apoptotic signaling pathway cell communication positive regulation of response to stimulus signal transduction positive regulation of cellular process cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction regulation of programmed cell death positive regulation of apoptotic signaling pathway cell communication positive regulation of response to stimulus signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of programmed cell death regulation of apoptotic process biological regulation cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication cellular process apoptotic process programmed cell death positive regulation of signaling 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 activation of cysteine-type endopeptidase activity involved in apoptotic process activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c 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 multicellular organismal process embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching anatomical structure development epithelial tube morphogenesis system development developmental process morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure catabolic process macromolecule catabolic process regulation of DNA catabolic process nucleobase-containing compound metabolic process cellular component organization execution phase of apoptosis DNA catabolic process apoptotic nuclear changes cellular component organization or biogenesis regulation of nucleobase-containing compound metabolic process regulation of apoptotic DNA fragmentation cellular component disassembly DNA metabolic process regulation of catabolic process organic cyclic compound catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process organic cyclic compound metabolic process apoptotic DNA fragmentation cellular component disassembly involved in execution phase of apoptosis nucleic acid catabolic process organic substance catabolic process regulation of DNA metabolic process response to G1 DNA damage checkpoint signaling response to endogenous stimulus response to mitotic cell cycle checkpoint signaling response to biotic stimulus cellular response to biotic stimulus cellular response to endogenous stimulus response to DNA integrity checkpoint signaling response to DNA damage checkpoint signaling response to cell cycle checkpoint signaling response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels response to abiotic stimulus animal organ development kidney development renal system development muscle cell apoptotic process striated muscle cell apoptotic process cardiac muscle cell apoptotic process cellular developmental process cell differentiation intracellular signal transduction intrinsic apoptotic signaling pathway cellular response to growth factor stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to growth factor head development forebrain development brain development central nervous system development neuron apoptotic process intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress cellular response to stress response to endoplasmic reticulum stress response to nutrient levels response to chemical response to nutrient	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle protein-containing complex apoptosome vesicle lumen cytoplasmic vesicle lumen secretory granule lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR019775	WD40 repeat, conserved site	Conserved Site
A, B, C, D	IPR037963	Apoptotic Protease-Activating Factor 1, CARD domain	Domain
A, B, C, D	IPR002182	NB-ARC	Domain
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D	IPR042197	Apoptotic protease-activating factors, helical domain	Homologous Superfamily
A, B, C, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, B, C, D	IPR048975	Apoptotic protease-activating factor 1, winged-helix domain	Domain
A, B, C, D	IPR020472	G-protein beta WD-40 repeat	Repeat
A, B, C, D	IPR017251	Apoptotic protease-activating factor 1	Family
A, B, C, D	IPR041452	APAF-1 helical domain	Domain
A, B, C, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B, C, D	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR001680	WD40 repeat	Repeat
A, B, C, D	IPR001315	CARD domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O14727	transitional cell carcinoma renal cell carcinoma retinal detachment Skin Abnormalities collecting duct carcinoma sarcomatoid renal cell carcinoma chromophobe renal cell carcinoma papillary renal cell carcinoma adrenal cortex carcinoma clear cell renal carcinoma hepatocellular carcinoma malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous neoplasm renal carcinoma cancer transitional cell carcinoma renal cell carcinoma retinal detachment Skin Abnormalities collecting duct carcinoma sarcomatoid renal cell carcinoma chromophobe renal cell carcinoma papillary renal cell carcinoma adrenal cortex carcinoma clear cell renal carcinoma hepatocellular carcinoma malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous neoplasm renal carcinoma cancer exocrine pancreatic carcinoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia major depressive disorder osteosarcoma