3V3K

Human caspase 9 in complex with bacterial effector protein

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	Caspase-like	8033660	3001096	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Caspase-like	8033660	3001096	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Caspase-like	8033660	3001096	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Caspase-like	8033660	3001096	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Caspase-like	8033660	3001096	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Caspase-like	8033660	3001096	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Caspase-like	8033660	3001096	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Caspase-like	8033660	3001096	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FlgN-like	8093005	3001299	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	FlgN-like	8093005	3001299	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	FlgN-like	8093005	3001299	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	FlgN-like	8093005	3001299	SCOP2B (2022-06-29)
J	SCOP2 Family	NleF-like	8046176	4004931	SCOP2 (2022-06-29)
J	SCOP2 Superfamily	FlgN-like	8093005	3001299	SCOP2 (2022-06-29)
L	SCOP2B Superfamily	FlgN-like	8093005	3001299	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	FlgN-like	8093005	3001299	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	FlgN-like	8093005	3001299	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	PF00656	e3v3kA1	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: PF00656	ECOD (1.6)
C	PF00656	e3v3kC2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: PF00656	ECOD (1.6)
E	PF00656	e3v3kE2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: PF00656	ECOD (1.6)
G	PF00656	e3v3kG2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: PF00656	ECOD (1.6)
I	PF00656	e3v3kI1	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: PF00656	ECOD (1.6)
K	PF00656	e3v3kK2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: PF00656	ECOD (1.6)
M	PF00656	e3v3kM1	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: PF00656	ECOD (1.6)
O	PF00656	e3v3kO2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: PF00656	ECOD (1.6)
B	PF16809	e3v3kB1	A: alpha bundles	X: Effector protein NleF (From Topology)	H: Effector protein NleF (From Topology)	T: Effector protein NleF	F: PF16809	ECOD (1.6)
D	PF16809	e3v3kD1	A: alpha bundles	X: Effector protein NleF (From Topology)	H: Effector protein NleF (From Topology)	T: Effector protein NleF	F: PF16809	ECOD (1.6)
F	PF16809	e3v3kF1	A: alpha bundles	X: Effector protein NleF (From Topology)	H: Effector protein NleF (From Topology)	T: Effector protein NleF	F: PF16809	ECOD (1.6)
H	PF16809	e3v3kH1	A: alpha bundles	X: Effector protein NleF (From Topology)	H: Effector protein NleF (From Topology)	T: Effector protein NleF	F: PF16809	ECOD (1.6)
J	PF16809	e3v3kJ1	A: alpha bundles	X: Effector protein NleF (From Topology)	H: Effector protein NleF (From Topology)	T: Effector protein NleF	F: PF16809	ECOD (1.6)
L	PF16809	e3v3kL1	A: alpha bundles	X: Effector protein NleF (From Topology)	H: Effector protein NleF (From Topology)	T: Effector protein NleF	F: PF16809	ECOD (1.6)
N	PF16809	e3v3kN1	A: alpha bundles	X: Effector protein NleF (From Topology)	H: Effector protein NleF (From Topology)	T: Effector protein NleF	F: PF16809	ECOD (1.6)
P	PF16809	e3v3kP1	A: alpha bundles	X: Effector protein NleF (From Topology)	H: Effector protein NleF (From Topology)	T: Effector protein NleF	F: PF16809	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
E	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
G	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
I	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
K	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
M	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
O	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	1.20.1260.90	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
D	1.20.1260.90	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
F	1.20.1260.90	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
H	1.20.1260.90	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
J	1.20.1260.90	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
L	1.20.1260.90	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
N	1.20.1260.90	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
P	1.20.1260.90	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K, M, O	PF00656	Caspase domain (Peptidase_C14)	Caspase domain	-	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	PF16809	NleF caspase inhibitor (NleF_casp_inhib)	NleF caspase inhibitor	Binds to and inhibits caspase-9, caspase-8 and caspase-4. therefore preventing caspase-induced apoptosis in the host cell [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K, M, O	Caspase-9	SH3 domain binding protein binding binding protein domain specific binding identical protein binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity enzyme regulator activity enzyme activator activity SH3 domain binding protein binding binding protein domain specific binding identical protein binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cysteine-type peptidase activity cysteine-type endopeptidase activity endopeptidase activity enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity kinase binding enzyme binding protein kinase binding cysteine-type endopeptidase activity involved in apoptotic process cysteine-type endopeptidase activity involved in apoptotic signaling pathway	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process leukocyte apoptotic process apoptotic process cell death programmed cell death response to ischemia glial cell apoptotic process regulation of biological process positive regulation of programmed cell death cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process leukocyte apoptotic process apoptotic process cell death programmed cell death response to ischemia glial cell apoptotic process regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death positive regulation of apoptotic process positive regulation of cellular process neuron apoptotic process positive regulation of neuron apoptotic process regulation of neuron apoptotic process 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 response to organic substance response to ketone response to lipid cellular response to endogenous stimulus response to hormone response to steroid hormone cellular response to organic substance cellular response to ketone cellular response to steroid hormone stimulus response to organic cyclic compound cellular response to hormone stimulus response to endogenous stimulus cellular response to dexamethasone stimulus response to glucocorticoid cellular response to organic cyclic compound cellular response to glucocorticoid stimulus response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to corticosteroid stimulus response to corticosteroid cellular response to chemical stimulus response to chemical cellular response to lipid response to dexamethasone fibroblast apoptotic process response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus developmental process multicellular organism development multicellular organismal process anatomical structure development animal organ development kidney development renal system development system development signaling intracellular signal transduction cell communication signal transduction in response to DNA damage signal transduction apoptotic signaling pathway intrinsic apoptotic signaling pathway epithelial cell apoptotic process cellular biosynthetic process cellular metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process organic substance biosynthetic process protein processing intrinsic apoptotic signaling pathway in response to DNA damage cellular developmental process hemopoiesis platelet morphogenesis cell development cell morphogenesis anatomical structure morphogenesis myeloid cell differentiation cell differentiation platelet formation anatomical structure formation involved in morphogenesis response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus response to radiation cellular response to abiotic stimulus cellular response to UV response to cobalt ion response to metal ion response to inorganic substance biological process involved in interspecies interaction between organisms response to other organism response to external stimulus response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin response to estradiol	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle protein-containing complex catalytic complex caspase complex peptidase complex endopeptidase complex intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle protein-containing complex catalytic complex caspase complex peptidase complex endopeptidase complex apoptosome nucleus
B, D, F, H, J B, D, F, H, J, L, N, P	Putative uncharacterized protein ECs1815	enzyme regulator activity molecular function inhibitor activity peptidase regulator activity molecular function regulator activity enzyme inhibitor activity peptidase inhibitor activity	-	extracellular region cellular anatomical entity host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K, M, O	IPR029030	Caspase-like domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR001309	Peptidase C14, p20 domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR011600	Peptidase C14, caspase domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR016129	Peptidase family C14A, His active site	Active Site
A, C, E, G, I A, C, E, G, I, K, M, O	IPR042147	CASP9, CARD domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR015917	Peptidase C14A, caspase catalytic domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR033139	Peptidase family C14A, cysteine active site	Active Site
A, C, E, G, I A, C, E, G, I, K, M, O	IPR002138	Peptidase C14, caspase non-catalytic subunit p10	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR001315	CARD domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR038334	NleF superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P	IPR031829	Effector protein NleF	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G, I A, C, E, G, I, K, M, O	Pharos: P55211	retinal detachment transient ischemic attack brain ischemia peripheral nervous system disease prostate cancer Edema peripheral neuropathy nervous system disorder tuberculosis adrenal cortex carcinoma cancer intestinal disease lymphatic system disease alcoholic pancreatitis liver disease retinal detachment transient ischemic attack brain ischemia peripheral nervous system disease prostate cancer Edema peripheral neuropathy nervous system disorder tuberculosis adrenal cortex carcinoma cancer intestinal disease lymphatic system disease alcoholic pancreatitis liver disease breast disease hematologic disease lung disease

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.