5GKN | pdb_00005gkn

Catalase structure determined by electron crystallography of thin 3D crystals

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Heme-dependent catalase-like	8037382	3001681	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Heme-dependent catalase-like	8037382	3001681	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Heme-dependent catalase-like	8037382	3001681	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Heme-dependent catalase-like	8037382	3001681	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)
D		e5gknD1	A: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: HTH_3	F:	ECOD (20:10:01)
C		e5gknC1	A: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: HTH_3	F:	ECOD (20:10:01)
B		e5gknB1	A: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: HTH_3	F:	ECOD (20:10:01)
A		e5gknA1	A: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: HTH_3	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	4.10.91.20	Few Secondary Structures	Irregular	Cytochrome C Oxidase	Chain J	CATH (4.3.0)
D	2.40.180.10	Mainly Beta	Beta Barrel	Catalase HpII, Chain A, domain 1	Catalase core domain	CATH (4.3.0)
D	1.20.1370.60	Mainly Alpha	Up-down Bundle	Hemocyanin, N-terminal domain		CATH (4.3.0)
C	4.10.91.20	Few Secondary Structures	Irregular	Cytochrome C Oxidase	Chain J	CATH (4.3.0)
C	2.40.180.10	Mainly Beta	Beta Barrel	Catalase HpII, Chain A, domain 1	Catalase core domain	CATH (4.3.0)
C	1.20.1370.60	Mainly Alpha	Up-down Bundle	Hemocyanin, N-terminal domain		CATH (4.3.0)
B	4.10.91.20	Few Secondary Structures	Irregular	Cytochrome C Oxidase	Chain J	CATH (4.3.0)
B	2.40.180.10	Mainly Beta	Beta Barrel	Catalase HpII, Chain A, domain 1	Catalase core domain	CATH (4.3.0)
B	1.20.1370.60	Mainly Alpha	Up-down Bundle	Hemocyanin, N-terminal domain		CATH (4.3.0)
A	4.10.91.20	Few Secondary Structures	Irregular	Cytochrome C Oxidase	Chain J	CATH (4.3.0)
A	2.40.180.10	Mainly Beta	Beta Barrel	Catalase HpII, Chain A, domain 1	Catalase core domain	CATH (4.3.0)
A	1.20.1370.60	Mainly Alpha	Up-down Bundle	Hemocyanin, N-terminal domain		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF06628	Catalase-related immune-responsive (Catalase-rel)	Catalase-related immune-responsive	-	Family
A, B, C, D	PF00199	Catalase (Catalase)	Catalase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Catalase	peroxidase activity oxidoreductase activity antioxidant activity catalase activity oxidoreductase activity, acting on peroxide as acceptor catalytic activity binding tetrapyrrole binding heme binding protein binding enzyme binding cation binding ion binding metal ion binding peroxidase activity oxidoreductase activity antioxidant activity catalase activity oxidoreductase activity, acting on peroxide as acceptor catalytic activity binding tetrapyrrole binding heme binding protein binding enzyme binding cation binding ion binding metal ion binding small molecule binding	catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process cellular process hydrogen peroxide catabolic process response to hydrogen peroxide response to oxidative stress response to stimulus response to stress response to chemical response to oxygen-containing compound response to reactive oxygen species regulation of biological process catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process cellular process hydrogen peroxide catabolic process response to hydrogen peroxide response to oxidative stress response to stimulus response to stress response to chemical response to oxygen-containing compound response to reactive oxygen species regulation of biological process regulation of cellular process positive regulation of cell division biological regulation positive regulation of biological process cell division positive regulation of cellular process regulation of cell division cellular response to stimulus cellular detoxification of hydrogen peroxide detoxification of inorganic compound detoxification cellular response to oxidative stress cellular response to chemical stress cellular oxidant detoxification cellular response to reactive oxygen species cellular response to stress cellular detoxification cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to toxic substance cellular response to chemical stimulus detoxification of hydrogen peroxide cellular response to toxic substance	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle peroxisome microbody catalase complex protein-containing complex catalytic complex oxidoreductase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle peroxisome microbody catalase complex protein-containing complex catalytic complex oxidoreductase complex peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen organelle lumen microbody lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR024708	Catalase active site	Active Site
A, B, C, D	IPR010582	Catalase immune-responsive domain	Domain
A, B, C, D	IPR002226	Catalase haem-binding site	Binding Site
A, B, C, D	IPR020835	Catalase superfamily	Homologous Superfamily
A, B, C, D	IPR024711	Catalase, mono-functional, haem-containing, clades 1 and 3	Family
A, B, C, D	IPR011614	Catalase core domain	Domain
A, B, C, D	IPR018028	Catalase, mono-functional, haem-containing	Family
A, B, C, D	IPR040333	Catalase, clade 3	Family

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.