5DF5 | pdb_00005df5

The structure of oxidized rat cytochrome c (T28E) at 1.30 angstroms resolution.

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)
D	d5df5d_	All alpha proteins	Cytochrome c	Cytochrome c	monodomain cytochrome c	automated matches	Norway Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d5df5c_	All alpha proteins	Cytochrome c	Cytochrome c	monodomain cytochrome c	automated matches	Norway Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d5df5b_	All alpha proteins	Cytochrome c	Cytochrome c	monodomain cytochrome c	automated matches	Norway Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d5df5a_	All alpha proteins	Cytochrome c	Cytochrome c	monodomain cytochrome c	automated matches	Norway Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Cytochrome c	8068521	3000815	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cytochrome c	8068521	3000815	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytochrome c	8068521	3000815	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cytochrome c	8068521	3000815	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	Pyridoxal_deC	e5df5D1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Pyridoxal_deC	ECOD (v294.1)
C	Pyridoxal_deC	e5df5C1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Pyridoxal_deC	ECOD (v294.1)
B	Pyridoxal_deC	e5df5B1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Pyridoxal_deC	ECOD (v294.1)
A	Pyridoxal_deC	e5df5A1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Pyridoxal_deC	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Cytochrome c, somatic	electron transfer activity binding tetrapyrrole binding heme binding protein binding enzyme binding cation binding ion binding metal ion binding small molecule 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 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 response to copper ion response to stimulus response to metal ion response to chemical hydrogen peroxide metabolic process reactive oxygen species metabolic process response to stress response to ischemia apoptotic process cell death programmed cell death glial cell apoptotic process reactive oxygen species biosynthetic process regulation of cellular process negative regulation of biological process negative regulation of reactive oxygen species metabolic process negative regulation of reactive oxygen species biosynthetic process regulation of hydrogen peroxide metabolic process negative regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of hydrogen peroxide biosynthetic process negative regulation of metabolic process biological regulation hydrogen peroxide biosynthetic process regulation of reactive oxygen species biosynthetic process negative regulation of hydrogen peroxide metabolic process biosynthetic process negative regulation of biosynthetic process negative regulation of hydrogen peroxide biosynthetic process regulation of metabolic process regulation of reactive oxygen species metabolic process response to auditory stimulus response to mechanical stimulus response to abiotic stimulus response to external stimulus response to carbon monoxide response to oxygen-containing compound response to oxidative stress response to gravity positive regulation of biological process regulation of generation of precursor metabolites and energy regulation of cellular respiration positive regulation of cellular respiration positive regulation of metabolic process positive regulation of cellular process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol protein-containing complex apoptosome mitochondrial intermembrane space membrane-enclosed lumen intracellular organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol protein-containing complex apoptosome mitochondrial intermembrane space membrane-enclosed lumen intracellular organelle lumen organelle envelope lumen organelle envelope organelle lumen mitochondrial envelope nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR002327	Cytochrome c, class IA/ IB	Family
A, B, C, D	IPR009056	Cytochrome c-like domain	Domain

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.