2YEV | pdb_00002yev

Structure of caa3-type cytochrome oxidase

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
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	FtsJ	e2yevF1	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: FtsJ	ECOD (develop294)
C	Tnp_22_dsRBD	e2yevC1	A: alpha bundles	X: dsRBD-like	H: C-terminal domain in LINE-1 ORF1p	T: C-terminal domain in LINE-1 ORF1p	F: Tnp_22_dsRBD	ECOD (develop294)
E	tRNA_anti-codon	e2yevE10	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: tRNA_anti-codon	ECOD (develop294)
B	MS_channel_2nd	e2yevB4	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: MS_channel_2nd	ECOD (develop294)
D	peroxidase	e2yevD1	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: peroxidase	ECOD (develop294)
A	Sina_ZnF	e2yevA4	A: alpha bundles	X: POZ domain	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Sina_ZnF	ECOD (develop294)
A	peroxidase	e2yevA2	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: peroxidase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	6.10.280.110	Special	Helix non-globular	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
C	6.10.280.110	Special	Helix non-globular	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
E	1.10.287.90	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
E	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
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	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)
D	1.10.287.70	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
D	1.20.120.80	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Cytochrome c oxidase, subunit III, four-helix bundle	CATH (4.3.0)
A	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (4.3.0)
A	1.10.287.70	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
A	1.20.120.80	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Cytochrome c oxidase, subunit III, four-helix bundle	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	PF20814	CAA3-type cytochrome c oxidase subunit IV (CAA3_Cox_suIV)	CAA3-type cytochrome c oxidase subunit IV	-	Family
B, E	PF00116	Cytochrome C oxidase subunit II, periplasmic domain (COX2)	Cytochrome C oxidase subunit II, periplasmic domain		Domain
B, E	PF02790	Cytochrome C oxidase subunit II, transmembrane domain (COX2_TM)	Cytochrome C oxidase subunit II, transmembrane domain	-	Family
B, E	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
A, D	PF00510	Cytochrome c oxidase subunit III (COX3)	Cytochrome c oxidase subunit III		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, F	CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV	-	-	-
B, E	CYTOCHROME C OXIDASE SUBUNIT 2	oxidoreductase activity catalytic 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 oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity binding oxidoreductase activity catalytic 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 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 cation binding transition metal ion binding copper ion binding ion binding metal ion binding small molecule binding	aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain ATP synthesis coupled electron transport electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cell periphery cellular anatomical structure plasma membrane membrane
A, D	CYTOCHROME C OXIDASE POLYPEPTIDE I+III	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 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 cation binding ion binding metal ion binding small molecule binding	electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport establishment of localization monoatomic cation transmembrane transport transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport aerobic respiration cellular respiration electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport establishment of localization monoatomic cation transmembrane transport 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 metabolic process generation of precursor metabolites and energy respiratory electron transport chain electron transport chain	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR038405	Cytochrome oxidase Caa3-type, subunit IV superfamily	Homologous Superfamily
C, F	IPR033793	Cytochrome oxidase Caa3-type, subunit IV	Domain
B, E	IPR011759	Cytochrome C oxidase subunit II, transmembrane domain	Domain
B, E	IPR036257	Cytochrome C oxidase subunit II, transmembrane domain superfamily	Homologous Superfamily
B, E	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
B, E	IPR045187	Cytochrome c/quinol oxidase subunit II	Family
B, E	IPR034236	Caa3-type Cytochrome c oxidase subunit II, cupredoxin domain	Domain
B, E	IPR009056	Cytochrome c-like domain	Domain
B, E	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
B, E	IPR008972	Cupredoxin	Homologous Superfamily
B, E	IPR001505	Copper centre Cu(A)	Binding Site
B, E	IPR014222	Cytochrome c oxidase, subunit II	Domain
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	IPR035973	Cytochrome c oxidase subunit III-like superfamily	Homologous Superfamily
A, D	IPR000298	Cytochrome c oxidase subunit III-like	Domain
A, D	IPR014241	Cytochrome c oxidase, subunit I bacterial type	Family
A, D	IPR013833	Cytochrome c oxidase, subunit III, 4-helical bundle	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, 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, C, D, E A, B, C, D, E, F	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, F	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)	Cytochrome C Oxidase, caa₃

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, F	FME	Parent Component: MET RESID: AA0021 , AA0566 PSI-MOD : N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891