3NKF | pdb_00003nkf

Crystal structure of human ligand-free mature caspase-6 with intersubunit linker attached

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)
D	SCOP2B Superfamily	Caspase-like	8081079	3001096	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Caspase-like	8081079	3001096	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Caspase-like	8081079	3001096	SCOP2B (2022-06-29)
A	SCOP2 Family	Caspase catalytic domain	8081078	4003593	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Caspase-like	8081079	3001096	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	FAD_binding_4	e3nkfD1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
C	FAD_binding_4	e3nkfC1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
B	FAD_binding_4	e3nkfB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
A	FAD_binding_4	e3nkfA1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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)
B	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00656	Caspase domain (Peptidase_C14)	Caspase domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Caspase-6	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity identical protein binding protein binding binding	regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus positive regulation of biological process response to biotic stimulus positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus positive regulation of biological process response to biotic stimulus positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of immune system process response to external biotic stimulus positive regulation of immune system process regulation of biological process positive regulation of innate immune response defense response immune response response to other organism regulation of innate immune response biological regulation defense response to symbiont response to external stimulus regulation of response to stimulus immune system process defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein autoprocessing biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus regulation of cellular process signaling signal transduction by p53 class mediator cell death intracellular signal transduction cell communication apoptotic signaling pathway intrinsic apoptotic signaling pathway by p53 class mediator signal transduction apoptotic process intrinsic apoptotic signaling pathway programmed cell death positive regulation of programmed cell death regulation of apoptotic 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 developmental process epithelium development cellular developmental process cell differentiation anatomical structure development tissue development epithelial cell differentiation cellular response to nitrogen compound cellular response to staurosporine response to staurosporine response to nitrogen compound response to alkaloid cellular response to chemical stimulus response to chemical cellular response to alkaloid hepatocyte apoptotic process epithelial cell apoptotic process positive regulation of necroptotic process necroptotic process programmed necrotic cell death regulation of necroptotic process regulation of programmed necrotic cell death positive regulation of programmed necrotic cell death pyroptotic inflammatory response inflammatory response	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR001309	Peptidase C14, p20 domain	Domain
A, B, C, D	IPR011600	Peptidase C14, caspase domain	Domain
A, B, C, D	IPR016129	Peptidase family C14A, His active site	Active Site
A, B, C, D	IPR015917	Peptidase C14A, caspase catalytic domain	Domain
A, B, C, D	IPR029030	Caspase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR033139	Peptidase family C14A, cysteine active site	Active Site
A, B, C, D	IPR002138	Peptidase C14, caspase non-catalytic subunit p10	Domain
A, B, C, D	IPR002398	Peptidase C14 family	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P55212	age-related macular degeneration glioblastoma lung cancer malignant mesothelioma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma ulcerative colitis atypical teratoid rhabdoid tumor invasive ductal breast carcinoma malignant ependymoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor wet macular degeneration ductal breast carcinoma in situ age-related macular degeneration glioblastoma lung cancer malignant mesothelioma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma ulcerative colitis atypical teratoid rhabdoid tumor invasive ductal breast carcinoma malignant ependymoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor wet macular degeneration ductal breast carcinoma in situ lung adenocarcinoma malignant glioma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia subependymal giant cell astrocytoma

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.