2QJY | pdb_00002qjy

Crystal structure of rhodobacter sphaeroides double mutant with stigmatellin and UQ2

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	ISP transmembrane anchor	8052868	3000753	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	ISP domain	8052870	3000233	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	ISP transmembrane anchor	8052868	3000753	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	ISP domain	8052870	3000233	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	ISP transmembrane anchor	8052868	3000753	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	ISP domain	8052870	3000233	SCOP2B (2022-06-29)
L	SCOP2 Family	TAT signal-like	8044808	4004149	SCOP2 (2022-06-29)
L	SCOP2 Family	Rieske iron-sulfur protein (ISP)	8052869	4001667	SCOP2 (2022-06-29)
L	SCOP2 Superfamily	ISP transmembrane anchor	8052868	3000753	SCOP2 (2022-06-29)
L	SCOP2 Superfamily	ISP domain	8052870	3000233	SCOP2 (2022-06-29)
I	SCOP2B Superfamily	ISP domain	8052870	3000233	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	ISP transmembrane anchor	8052868	3000753	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ISP transmembrane anchor	8052868	3000753	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ISP domain	8052870	3000233	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytochrome c	8099084	3000815	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor	8101132	3000762	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor	8101132	3000762	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Cytochrome c	8099084	3000815	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Cytochrome c	8099084	3000815	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor	8101132	3000762	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Cytochrome c	8099084	3000815	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor	8101132	3000762	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Cytochrome c	8099084	3000815	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor	8101132	3000762	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cytochrome c	8099084	3000815	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor	8101132	3000762	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	GFO_IDH_MocA	e2qjyF2	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: GFO_IDH_MocA	ECOD (develop294)
F	Ribonuc_red_lgN	e2qjyF4	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ribonuc_red_lgN	ECOD (develop294)
O	GFO_IDH_MocA	e2qjyO2	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: GFO_IDH_MocA	ECOD (develop294)
O	Ribonuc_red_lgN	e2qjyO3	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ribonuc_red_lgN	ECOD (develop294)
R	GFO_IDH_MocA	e2qjyR2	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: GFO_IDH_MocA	ECOD (develop294)
R	Ribonuc_red_lgN	e2qjyR3	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ribonuc_red_lgN	ECOD (develop294)
L	GFO_IDH_MocA	e2qjyL2	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: GFO_IDH_MocA	ECOD (develop294)
L	Ribonuc_red_lgN	e2qjyL4	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ribonuc_red_lgN	ECOD (develop294)
I	GFO_IDH_MocA	e2qjyI2	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: GFO_IDH_MocA	ECOD (develop294)
I	Ribonuc_red_lgN	e2qjyI3	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ribonuc_red_lgN	ECOD (develop294)
C	Ribonuc_red_lgN	e2qjyC1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ribonuc_red_lgN	ECOD (develop294)
B	ADAM_CR	e2qjyB1	A: alpha bundles	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: ADAM_CR	ECOD (develop294)
Q	ADAM_CR	e2qjyQ1	A: alpha bundles	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: ADAM_CR	ECOD (develop294)
N	ADAM_CR	e2qjyN1	A: alpha bundles	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: ADAM_CR	ECOD (develop294)
K	ADAM_CR	e2qjyK1	A: alpha bundles	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: ADAM_CR	ECOD (develop294)
H	ADAM_CR	e2qjyH1	A: alpha bundles	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: ADAM_CR	ECOD (develop294)
E	ADAM_CR	e2qjyE1	A: alpha bundles	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: ADAM_CR	ECOD (develop294)
P	Abhydrolase_1	e2qjyP2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Abhydrolase_1	ECOD (develop294)
P	Peptidase_S8	e2qjyP3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_S8	ECOD (develop294)
M	Abhydrolase_1	e2qjyM2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Abhydrolase_1	ECOD (develop294)
M	Peptidase_S8	e2qjyM3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_S8	ECOD (develop294)
J	Abhydrolase_1	e2qjyJ2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Abhydrolase_1	ECOD (develop294)
J	Peptidase_S8	e2qjyJ3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_S8	ECOD (develop294)
G	Abhydrolase_1	e2qjyG2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Abhydrolase_1	ECOD (develop294)
G	Peptidase_S8	e2qjyG3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_S8	ECOD (develop294)
D	Abhydrolase_1	e2qjyD2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Abhydrolase_1	ECOD (develop294)
D	Peptidase_S8	e2qjyD3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_S8	ECOD (develop294)
A	Abhydrolase_1	e2qjyA2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Abhydrolase_1	ECOD (develop294)
A	Peptidase_S8	e2qjyA3	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_S8	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	1.20.5.510	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
F	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
O	1.20.5.510	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
O	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
R	1.20.5.510	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
R	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
L	1.20.5.510	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
L	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
I	1.20.5.510	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
I	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
C	1.20.5.510	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
C	2.102.10.10	Mainly Beta	3-layer Sandwich	Rieske Iron-sulfur Protein	Rieske [2Fe-2S] iron-sulphur domain	CATH (4.3.0)
B	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
B	1.20.5.100	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Cytochrome c1, transmembrane anchor, C-terminal	CATH (4.3.0)
Q	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
Q	1.20.5.100	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Cytochrome c1, transmembrane anchor, C-terminal	CATH (4.3.0)
N	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
N	1.20.5.100	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Cytochrome c1, transmembrane anchor, C-terminal	CATH (4.3.0)
K	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
K	1.20.5.100	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Cytochrome c1, transmembrane anchor, C-terminal	CATH (4.3.0)
H	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
H	1.20.5.100	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Cytochrome c1, transmembrane anchor, C-terminal	CATH (4.3.0)
E	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
E	1.20.5.100	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Cytochrome c1, transmembrane anchor, C-terminal	CATH (4.3.0)
P	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (4.3.0)
M	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (4.3.0)
J	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (4.3.0)
G	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (4.3.0)
D	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (4.3.0)
A	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I, L, O C, F, I, L, O, R	Ubiquinol-cytochrome c reductase iron-sulfur subunit	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	cell periphery cellular anatomical structure plasma membrane membrane
B, E, H, K, N B, E, H, K, N, Q	Cytochrome c1	binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	cell periphery cellular anatomical structure plasma membrane membrane
A, D, G, J, M A, D, G, J, M, P	Cytochrome b	oxidoreductase activity catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity cation binding oxidoreductase activity catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	respiratory chain complex protein-containing complex cellular anatomical structure cytochrome complex catalytic complex transmembrane transporter complex membrane membrane protein complex transporter complex respiratory chain complex III cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F, I, L, O C, F, I, L, O, R	IPR017941	Rieske [2Fe-2S] iron-sulphur domain	Domain
C, F, I, L, O C, F, I, L, O, R	IPR005805	Rieske iron-sulphur protein, C-terminal	Domain
C, F, I, L, O C, F, I, L, O, R	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily	Homologous Superfamily
C, F, I, L, O C, F, I, L, O, R	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
C, F, I, L, O C, F, I, L, O, R	IPR014349	Rieske iron-sulphur protein	Family
C, F, I, L, O C, F, I, L, O, R	IPR019470	Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal	Domain
C, F, I, L, O C, F, I, L, O, R	IPR006317	Ubiquinol-cytochrome c reductase, iron-sulphur subunit	Domain
C, F, I, L, O C, F, I, L, O, R	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site
B, E, H, K, N B, E, H, K, N, Q	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
B, E, H, K, N B, E, H, K, N, Q	IPR002326	Cytochrome c1	Family
B, E, H, K, N B, E, H, K, N, Q	IPR009056	Cytochrome c-like domain	Domain
A, D, G, J, M A, D, G, J, M, P	IPR036150	Cytochrome b/b6, C-terminal domain superfamily	Homologous Superfamily
A, D, G, J, M A, D, G, J, M, P	IPR027387	Cytochrome b/b6-like domain superfamily	Homologous Superfamily
A, D, G, J, M A, D, G, J, M, P	IPR048260	Cytochrome b/b6, C-terminal domain, eukaryotic/bacterial	Domain
A, D, G, J, M A, D, G, J, M, P	IPR016174	Di-haem cytochrome, transmembrane	Homologous Superfamily
A, D, G, J, M A, D, G, J, M, P	IPR005798	Cytochrome b/b6, C-terminal	Domain
A, D, G, J, M A, D, G, J, M, P	IPR048259	Cytochrome b/b6, N-terminal domain, eukaryotic/bacterial	Domain
A, D, G, J, M A, D, G, J, M, P	IPR030689	Cytochrome b	Family
A, D, G, J, M A, D, G, J, M, P	IPR005797	Cytochrome b/b6, N-terminal domain	Domain

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, G, H, I, J, K, L, M, N, O, P, Q, R	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex III (bc1 and b6f) superfamily	Cytochrome bc1 and b6f complexes

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	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, G, H, I, J, K, L, M, N, O, P, Q, R	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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