6RKO | pdb_00006rko

Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 A resolution

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	Ribosomal_S20p	e6rkoB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Ribosomal_S20p	ECOD (v294.1)
B [auth A]	Ribosomal_S20p	e6rkoA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Ribosomal_S20p	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF02322	Cytochrome bd terminal oxidase subunit II (Cyt_bd_oxida_II)	Cytochrome bd terminal oxidase subunit II	-	Family
B [auth A]	PF01654	Cytochrome bd terminal oxidase subunit I (Cyt_bd_oxida_I)	Cytochrome bd terminal oxidase subunit I	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Cytochrome bd-I ubiquinol oxidase subunit 2	oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor oxidoreductase activity oxidoreductase activity, acting on diphenols and related substances as donors catalytic activity electron transfer activity cation binding ion binding binding metal ion binding small molecule binding	aerobic electron transport chain aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex cytochrome complex catalytic complex
B [auth A]	Cytochrome bd-I ubiquinol oxidase subunit 1	oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor oxidoreductase activity oxidoreductase activity, acting on diphenols and related substances as donors catalytic activity binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	aerobic electron transport chain aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex cytochrome complex catalytic complex
C [auth H]	Uncharacterized protein YnhF	-	response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus cellular process	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex cytochrome complex catalytic complex
D [auth X]	Cytochrome bd-I ubiquinol oxidase subunit X	oxidoreductase activity oxidoreductase activity, acting on diphenols and related substances as donors catalytic activity	aerobic electron transport chain aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cell periphery cellular anatomical structure plasma membrane membrane outer membrane protein-containing complex cytochrome complex catalytic complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR003317	Cytochrome ubiquinol oxidase subunit 2	Family
B [auth A]	IPR002585	Cytochrome ubiquinol oxidase subunit 1	Family
C [auth H]	IPR047743	Membrane protein YnhF-like	Family
D [auth X]	IPR011724	Cyd operon protein YbgT	Family
D [auth X]	IPR012994	Membrane bound YbgT-like	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth B], B [auth A], C [auth H], D [auth X]	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex IV (cytochrome c oxidase)	Cytochrome BD oxidase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth B], B [auth A], C [auth H], D [auth X]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth B], B [auth A], C [auth H], D [auth X]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth B], B [auth A], C [auth H], D [auth X]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)	Cytochrome bd-type oxidase in nanodiscs

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.