1QLE

CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1qlea_	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	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
B	d1qleb1	All beta proteins	Cupredoxin-like	Cupredoxins	Periplasmic domain of cytochrome c oxidase subunit II	Cytochrome c oxidase	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
B	d1qleb2	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	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
C	d1qlec_	Membrane and cell surface proteins and peptides	Cytochrome c oxidase subunit III-like	Cytochrome c oxidase subunit III-like	Cytochrome c oxidase subunit III-like	Bacterial aa3 type cytochrome c oxidase subunit III	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
D	d1qled_	Membrane and cell surface proteins and peptides	Single transmembrane helix	Bacterial aa3 type cytochrome c oxidase subunit IV	Bacterial aa3 type cytochrome c oxidase subunit IV	Bacterial aa3 type cytochrome c oxidase subunit IV	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
E [auth H]	d1qleh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth L]	d1qlel_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cytochrome c oxidase subunit I-like	8037803	3000653	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytochrome c oxidase subunit II-like, transmembrane region	8041054	3000692	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cupredoxins	8041053	3000886	SCOP2B (2022-06-29)
C	SCOP2 Family	Cytochrome c oxidase subunit III-like	8025427	4002000	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Cytochrome c oxidase subunit III-like	8037806	3000671	SCOP2 (2022-06-29)
D	SCOP2 Family	Bacterial aa3 type cytochrome c oxidase subunit IV	8025428	4002018	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Bacterial aa3 type cytochrome c oxidase subunit IV	8037807	3000704	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	COX1	e1qleA1	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)
B	COX2	e1qleB1	A: beta sandwiches	X: Cupredoxin-like	H: Cupredoxin-related (From Topology)	T: Cupredoxin-related	F: COX2	ECOD (1.6)
B	COX2_TM	e1qleB2	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	COX3	e1qleC1	A: alpha bundles	X: Cytochrome c oxidase subunit III-like (From Topology)	H: Cytochrome c oxidase subunit III-like (From Topology)	T: Cytochrome c oxidase subunit III-like	F: COX3	ECOD (1.6)
D	COX4_pro_2	e1qleD1	A: extended segments	X: Bacterial aa3 type cytochrome c oxidase subunit IV (From Topology)	H: Bacterial aa3 type cytochrome c oxidase subunit IV (From Topology)	T: Bacterial aa3 type cytochrome c oxidase subunit IV	F: COX4_pro_2	ECOD (1.6)
E [auth H]	V-set_8	e1qleH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
F [auth L]	V-set	e1qleL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	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	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)
C	1.10.287.70	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
C	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)
D	1.20.5.160	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Bacterial aa3 type cytochrome c oxidase subunit IV	CATH (4.3.0)
E [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
E [auth H]	7E2C50S	VH	Mus musculus (house mouse)	IGHV5-12-201, IGHJ401	V-DOMAIN VH	IG	FV-HEAVY_KAPPA	IMGT (202449-0)
F [auth L]	7E2C50S	V-KAPPA	Mus musculus (house mouse)	IGKV12-4401, IGKJ101, IGKJ2*01	V-DOMAIN V-KAPPA	IG	FV-HEAVY_KAPPA	IMGT (202449-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth H]	Heavy Chain	IGHV5	-	cytochrome c oxidase polypeptide ii	SAbDab (2024-12-13)
F [auth L]	Light Chain	IGKV12	Kappa	cytochrome c oxidase polypeptide ii	SAbDab (2024-12-13)

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	PF02790	Cytochrome C oxidase subunit II, transmembrane domain (COX2_TM)	Cytochrome C oxidase subunit II, transmembrane domain	-	Family
C	PF00510	Cytochrome c oxidase subunit III (COX3)	Cytochrome c oxidase subunit III	-	Family
D	PF07835	Bacterial aa3 type cytochrome c oxidase subunit IV (COX4_pro_2)	Bacterial aa3 type cytochrome c oxidase subunit IV	Bacterial cytochrome c oxidase is found bound to the to the cell membrane, where it is involved in the generation of the transmembrane proton electrochemical gradient. It is composed of four subunits. Subunit IV consists of one transmembrane helix ...	Bacterial cytochrome c oxidase is found bound to the to the cell membrane, where it is involved in the generation of the transmembrane proton electrochemical gradient. It is composed of four subunits. Subunit IV consists of one transmembrane helix that does not interact directly with the other subunits, but maintains its position by indirect contacts via phospholipid molecules found in the structure. The function of subunit IV is as yet unknown [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CYTOCHROME C OXIDASE POLYPEPTIDE I-BETA	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 metabolic process generation of precursor metabolites and energy respiratory electron transport chain electron transport chain	respiratory chain complex protein-containing complex catalytic complex cytochrome complex membrane membrane protein complex respiratory chain complex IV transporter complex cellular anatomical structure transmembrane transporter complex oxidoreductase complex cell periphery plasma membrane
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	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
C	CYTOCHROME C OXIDASE POLYPEPTIDE 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 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	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
D	CCYTOCHROME C OXIDASE	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 cellular anatomical structure plasma membrane membrane
E [auth H]	HEAVY CHAIN ANTIBODY FV FRAGMENT	-	-	-
F [auth L]	LIGHT CHAIN ANTIBODY FV FRAGMENT	-	-	-

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	IPR033944	Cytochrome c oxidase subunit I domain	Domain
A	IPR014241	Cytochrome c oxidase, subunit I bacterial type	Family
B	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
B	IPR011759	Cytochrome C oxidase subunit II, transmembrane domain	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	IPR045187	Cytochrome c/quinol oxidase subunit II	Family
B	IPR014222	Cytochrome c oxidase, subunit II	Domain
C	IPR035973	Cytochrome c oxidase subunit III-like superfamily	Homologous Superfamily
C	IPR013833	Cytochrome c oxidase, subunit III, 4-helical bundle	Homologous Superfamily
C	IPR000298	Cytochrome c oxidase subunit III-like	Domain
C	IPR033945	Cytochrome c oxidase subunit III domain	Domain
C	IPR024791	Cytochrome c oxidase subunit III	Family
D	IPR012422	Cytochrome c oxidase, subunit IV, bacterial aa3 type	Domain
D	IPR036596	Bacterial aa3 type cytochrome c oxidase subunit IV superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	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	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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)	Cytochrome C Oxidase, aa₃, Fully Oxidized