2B12 | pdb_00002b12

Crystal structure of the protein-protein complex between F82Y cytochrome c and cytochrome c peroxidase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2b12b1	All alpha proteins	Cytochrome c	Cytochrome c	monodomain cytochrome c	Mitochondrial cytochrome c	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d2b12a_	All alpha proteins	Heme-dependent peroxidases	Heme-dependent peroxidases	CCP-like	Cytochrome c peroxidase, CCP	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Cytochrome c	8036427	3000815	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Heme-dependent peroxidases	8035554	3000844	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	MgsA_C	e2b12B1	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: MgsA_C	ECOD (develop294)
A	Ion_trans_2	e2b12A1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Ion_trans_2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
A	1.10.520.10	Mainly Alpha	Orthogonal Bundle	Peroxidase	domain 1	CATH (4.3.0)
A	1.10.420.10	Mainly Alpha	Orthogonal Bundle	Peroxidase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00034	Cytochrome c (Cytochrom_C)	Cytochrome c	The Pfam entry does not include all Prosite members. The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, Pfam:PF06181, has now been merged into this family.	Domain
A	PF00141	Peroxidase (peroxidase)	Peroxidase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Cytochrome c iso-1	ion binding binding anion binding phosphatidylglycerol binding phospholipid binding lipid binding cardiolipin binding small molecule binding tetrapyrrole binding heme binding electron transfer activity cation binding metal ion binding	aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy mitochondrial electron transport, cytochrome c to oxygen respiratory electron transport chain metabolic process cellular process mitochondrial ATP synthesis coupled electron transport mitochondrial electron transport, ubiquinol to cytochrome c	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial intermembrane space membrane-enclosed lumen intracellular organelle lumen organelle envelope lumen organelle envelope organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial intermembrane space membrane-enclosed lumen intracellular organelle lumen organelle envelope lumen organelle envelope organelle lumen mitochondrial envelope
A	Cytochrome c peroxidase, mitochondrial	peroxidase activity oxidoreductase activity antioxidant activity oxidoreductase activity, acting on peroxide as acceptor catalytic activity binding tetrapyrrole binding heme binding cytochrome-c peroxidase activity 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 oxidative stress response to stimulus response to stress response to chemical response to oxygen-containing compound response to reactive oxygen species cellular response to stimulus cellular response to chemical stimulus catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process cellular process hydrogen peroxide catabolic process response to oxidative stress response to stimulus response to stress response to chemical response to oxygen-containing compound response to reactive oxygen species cellular response to stimulus cellular response to chemical stimulus cellular response to stress cellular response to oxidative stress cellular response to chemical stress	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen mitochondrial intermembrane space organelle envelope lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen mitochondrial intermembrane space organelle envelope lumen organelle envelope mitochondrial envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
B	IPR009056	Cytochrome c-like domain	Domain
B	IPR002327	Cytochrome c, class IA/ IB	Family
A	IPR002016	Haem peroxidase	Domain
A	IPR019794	Peroxidase, active site	Active Site
A	IPR010255	Haem peroxidase superfamily	Homologous Superfamily
A	IPR002207	Class I peroxidase	Family
A	IPR044831	Heme-binding peroxidase Ccp1-like	Family
A	IPR019793	Peroxidases heam-ligand binding site	Binding Site

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.