3DTU

Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides complexed with deoxycholic acid

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)
B	d3dtub1	All beta proteins	Cupredoxin-like	Cupredoxins	Periplasmic domain of cytochrome c oxidase subunit II	Cytochrome c oxidase	Rhodopseudomonas sphaeroides (Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
B	d3dtub2	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 aa3 type cytochrome c oxidase subunit II	Rhodopseudomonas sphaeroides (Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
B	d3dtub3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Rhodopseudomonas sphaeroides (Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
D	d3dtud1	All beta proteins	Cupredoxin-like	Cupredoxins	Periplasmic domain of cytochrome c oxidase subunit II	Cytochrome c oxidase	Rhodopseudomonas sphaeroides (Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
D	d3dtud2	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 aa3 type cytochrome c oxidase subunit II	Rhodopseudomonas sphaeroides (Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
D	d3dtud3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Rhodopseudomonas sphaeroides (Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
C	d3dtuc_	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 aa3 type cytochrome c oxidase subunit I	Rhodopseudomonas sphaeroides (Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
A	d3dtua_	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 aa3 type cytochrome c oxidase subunit I	Rhodopseudomonas sphaeroides (Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Cytochrome c oxidase subunit II-like transmembrane region	8028517	4002011	SCOP2 (2022-06-29)
B	SCOP2 Family	Periplasmic domain of cytochrome c oxidase subunit II	8028512	4002191	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cytochrome c oxidase subunit II-like transmembrane region	8040896	3000692	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cupredoxins	8040891	3000886	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Cupredoxins	8040891	3000886	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cytochrome c oxidase subunit II-like transmembrane region	8040896	3000692	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cytochrome c oxidase subunit I-like	8040887	3000653	SCOP2B (2022-06-29)
A	SCOP2 Family	Cytochrome c oxidase subunit I-like	8028508	4001989	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cytochrome c oxidase subunit I-like	8040887	3000653	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)
B	COX2	e3dtuB1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
B	COX2_TM	e3dtuB2	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: COX2_TM	ECOD (1.6)
D	COX2	e3dtuD1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
D	COX2_TM	e3dtuD2	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: COX2_TM	ECOD (1.6)
C	COX1	e3dtuC1	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	e3dtuA1	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)
B	1.10.287.90	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
B	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
D	1.10.287.90	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
D	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
C	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)
A	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF00116	Cytochrome C oxidase subunit II, periplasmic domain (COX2)	Cytochrome C oxidase subunit II, periplasmic domain	-	Domain
B, D	PF02790	Cytochrome C oxidase subunit II, transmembrane domain (COX2_TM)	Cytochrome C oxidase subunit II, transmembrane domain	-	Family
A, C	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
B, D	Cytochrome c oxidase subunit 2	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
A, C	Cytochrome c oxidase subunit 1	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	electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds cellular metabolic process metabolic process generation of precursor metabolites and energy	respiratory chain complex protein-containing complex cytochrome complex catalytic complex membrane membrane protein complex respirasome respiratory chain complex IV cellular anatomical entity cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
B, D	IPR011759	Cytochrome C oxidase subunit II, transmembrane domain	Domain
B, D	IPR036257	Cytochrome C oxidase subunit II, transmembrane domain superfamily	Homologous Superfamily
B, D	IPR008972	Cupredoxin	Homologous Superfamily
B, D	IPR001505	Copper centre Cu(A)	Binding Site
B, D	IPR045187	Cytochrome c/quinol oxidase subunit II	Family
B, D	IPR014222	Cytochrome c oxidase, subunit II	Domain
A, C	IPR036927	Cytochrome c oxidase-like, subunit I superfamily	Homologous Superfamily
A, C	IPR000883	Cytochrome c oxidase subunit I	Family
A, C	IPR023615	Cytochrome c oxidase, subunit I, copper-binding site	Binding Site
A, C	IPR023616	Cytochrome c oxidase-like, subunit I domain	Domain
A, C	IPR033944	Cytochrome c oxidase subunit I domain	Domain
A, C	IPR014241	Cytochrome c oxidase, subunit I bacterial type	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D	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.