1XME

Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus

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
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1xmea_	Membrane and cell surface proteins and peptides	Cytochrome c oxidase subunit I-like	Cytochrome c oxidase subunit I-like	Cytochrome c oxidase subunit I-like	Bacterial ba3 type cytochrome c oxidase subunit I	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1xmeb1	All beta proteins	Cupredoxin-like	Cupredoxins	Periplasmic domain of cytochrome c oxidase subunit II	Cytochrome c oxidase	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1xmeb2	Membrane and cell surface proteins and peptides	Transmembrane helix hairpin	Cytochrome c oxidase subunit II-like, transmembrane region	Cytochrome c oxidase subunit II-like, transmembrane region	Bacterial ba3 type cytochrome c oxidase subunit II	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C	d1xmec_	Membrane and cell surface proteins and peptides	Single transmembrane helix	Bacterial ba3 type cytochrome c oxidase subunit IIa	Bacterial ba3 type cytochrome c oxidase subunit IIa	Bacterial ba3 type cytochrome c oxidase subunit IIa	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Cytochrome c oxidase subunit I-like	8021416	4001989	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cytochrome c oxidase subunit I-like	8033796	3000653	SCOP2 (2022-06-29)
B	SCOP2 Family	Cytochrome c oxidase subunit II-like transmembrane region	8021418	4002011	SCOP2 (2022-06-29)
B	SCOP2 Family	Periplasmic domain of cytochrome c oxidase subunit II	8028202	4002191	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cytochrome c oxidase subunit II-like transmembrane region	8033798	3000692	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cupredoxins	8040581	3000886	SCOP2 (2022-06-29)
C	SCOP2 Family	Bacterial ba3 type cytochrome c oxidase subunit IIa	8021419	4002024	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Bacterial ba3 type cytochrome c oxidase subunit IIa	8033799	3000717	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00115	e1xmeA1	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: PF00115	ECOD (1.6)
B	PF00116	e1xmeB1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: PF00116	ECOD (1.6)
B	PF09125	e1xmeB2	A: extended segments	X: Cytochrome c oxidase subunit II-like, transmembrane region (From Topology)	H: Cytochrome c oxidase subunit II-like, transmembrane region (From Topology)	T: Cytochrome c oxidase subunit II-like, transmembrane region	F: PF09125	ECOD (1.6)
C	PF08113	e1xmeC1	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: PF08113	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)
B	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)
B	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00115	Cytochrome C and Quinol oxidase polypeptide I (COX1)	Cytochrome C and Quinol oxidase polypeptide I	-	Family
B	PF00116	Cytochrome C oxidase subunit II, periplasmic domain (COX2)	Cytochrome C oxidase subunit II, periplasmic domain	-	Domain
B	PF09125	Cytochrome C oxidase subunit II, transmembrane (COX2-transmemb)	Cytochrome C oxidase subunit II, transmembrane	Members of this family adopt a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold [1].	Domain
C	PF08113	Cytochrome c oxidase subunit IIa family (CoxIIa)	Cytochrome c oxidase subunit IIa family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Cytochrome c oxidase polypeptide 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 oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity 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 oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity binding organic cyclic compound binding tetrapyrrole binding heme binding cation binding ion binding metal ion binding small molecule binding	aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds cellular metabolic process metabolic process cellular process generation of precursor metabolites and energy	cell periphery plasma membrane membrane cellular anatomical entity respirasome
B	Cytochrome c oxidase polypeptide 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 oxidoreductase 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 oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity	-	cell periphery plasma membrane membrane cellular anatomical entity respirasome
C	Cytochrome c oxidase polypeptide IIA	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 oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity 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 oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity	-	cell periphery plasma membrane membrane cellular anatomical entity respirasome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036927	Cytochrome c oxidase-like, subunit I superfamily	Homologous Superfamily
A	IPR000883	Cytochrome c oxidase subunit I	Family
A	IPR023615	Cytochrome c oxidase, subunit I, copper-binding site	Binding Site
A	IPR023616	Cytochrome c oxidase-like, subunit I domain	Domain
A	IPR033943	Ba3-like heme-copper oxidase subunit I	Family
B	IPR015209	Cytochrome C oxidase subunit IIa, transmembrane domain	Domain
B	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
B	IPR036257	Cytochrome C oxidase subunit II, transmembrane domain superfamily	Homologous Superfamily
B	IPR008972	Cupredoxin	Homologous Superfamily
B	IPR001505	Copper centre Cu(A)	Binding Site
B	IPR034214	Ba3-like heme-copper oxidase subunit II, C-terminal	Domain
C	IPR012538	Cytochrome c oxidase polypeptide 2A	Family
C	IPR036246	Cytochrome c oxidase polypeptide 2A, ba3 type	Homologous Superfamily

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C	MemProtMD	Annotated as membrane protein by MemProtMD

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.