7DEG | pdb_00007deg

Cryo-EM structure of a heme-copper terminal oxidase dimer provides insights into its catalytic mechanism

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth E]	COX2	e7degE1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
C [auth B]	COX2	e7degB1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
E [auth F]	F_UNCLASSIFIED	e7degF1	A: extended segments	X: Bacterial ba3 type cytochrome c oxidase subunit IIa (From Topology)	H: Bacterial ba3 type cytochrome c oxidase subunit IIa (From Topology)	T: Bacterial ba3 type cytochrome c oxidase subunit IIa	F: F_UNCLASSIFIED	ECOD (1.6)
B [auth C]	F_UNCLASSIFIED	e7degC1	A: extended segments	X: Bacterial ba3 type cytochrome c oxidase subunit IIa (From Topology)	H: Bacterial ba3 type cytochrome c oxidase subunit IIa (From Topology)	T: Bacterial ba3 type cytochrome c oxidase subunit IIa	F: F_UNCLASSIFIED	ECOD (1.6)
D	COX1	e7degD1	A: alpha superhelices	X: Cytochrome c oxidase subunit I-like	H: Cytochrome c oxidase subunit I-like (From Topology)	T: Cytochrome c oxidase subunit I-like	F: COX1	ECOD (1.6)
A	COX1	e7degA1	A: alpha superhelices	X: Cytochrome c oxidase subunit I-like	H: Cytochrome c oxidase subunit I-like (From Topology)	T: Cytochrome c oxidase subunit I-like	F: COX1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (utative)
A	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth B], F [auth E]	PF00116	Cytochrome C oxidase subunit II, periplasmic domain (COX2)	Cytochrome C oxidase subunit II, periplasmic domain		Domain
A, D	PF00115	Cytochrome C and Quinol oxidase polypeptide I (COX1)	Cytochrome C and Quinol oxidase polypeptide I	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth B], F [auth E]	Cytochrome oxidase subunit II	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	-	cellular anatomical structure membrane cell envelope
B [auth C], E [auth F]	Cytochrome oxidase subunit IIa	-	-	cellular anatomical structure membrane
A, D	Cytochrome c oxidase subunit I	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity binding tetrapyrrole binding heme binding	aerobic respiration cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth B], F [auth E]	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
C [auth B], F [auth E]	IPR008972	Cupredoxin	Homologous Superfamily
C [auth B], F [auth E]	IPR001505	Copper centre Cu(A)	Binding Site
C [auth B], F [auth E]	IPR034214	Ba3-like heme-copper oxidase subunit II, C-terminal	Domain
C [auth B], F [auth E]	IPR051403	NosZ/Cytochrome c oxidase subunit 2	Family
A, D	IPR036927	Cytochrome c oxidase-like, subunit I superfamily	Homologous Superfamily
A, D	IPR000883	Cytochrome c oxidase subunit I	Family
A, D	IPR023615	Cytochrome c oxidase, subunit I, copper-binding site	Binding Site
A, D	IPR023616	Cytochrome c oxidase-like, subunit I domain	Domain
A, D	IPR033943	Ba3-like heme-copper oxidase subunit I	Family

Membrane Protein Annotation: OPM OPM Database Homepage

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

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

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.