Annotations: 7YML

Structure of photosynthetic LH1-RC super-complex of Rhodobacter capsulatus

External Resource: Annotation

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: 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)
W [auth Z]	FAD_binding_4	e7ymlZ1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
U [auth W]	FAD_binding_4	e7ymlW1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
S [auth T]	FAD_binding_4	e7ymlT1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
Q [auth R]	FAD_binding_4	e7ymlR1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
O [auth P]	FAD_binding_4	e7ymlP1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
M [auth N]	FAD_binding_4	e7ymlN1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
K [auth J]	FAD_binding_4	e7ymlJ1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
I [auth G]	FAD_binding_4	e7ymlG1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
G [auth E]	FAD_binding_4	e7ymlE1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
E [auth B]	FAD_binding_4	e7ymlB1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
V [auth Y]	FAD_binding_4	e7ymlY1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
T [auth V]	FAD_binding_4	e7ymlV1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
R [auth S]	FAD_binding_4	e7ymlS1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
P [auth Q]	FAD_binding_4	e7ymlQ1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
N [auth O]	FAD_binding_4	e7ymlO1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
L [auth K]	FAD_binding_4	e7ymlK1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
J [auth I]	FAD_binding_4	e7ymlI1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
H [auth F]	FAD_binding_4	e7ymlF1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
F [auth D]	FAD_binding_4	e7ymlD1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
D [auth A]	FAD_binding_4	e7ymlA1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
C [auth H]	FAD_binding_4	e7ymlH1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
B [auth M]	FAD_binding_4	e7ymlM1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)
A [auth L]	FAD_binding_4	e7ymlL1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: FAD_binding_4	ECOD (v295)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth H]	3.90.50.10	Alpha Beta	Alpha-Beta Complex	Photosynthetic Reaction Center	Chain H, domain 2	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
X	Photosynthetic reaction center PufX protein	-	photosynthesis metabolic process cellular process	cell periphery cellular anatomical structure plasma membrane membrane
E [auth B], G [auth E], I [auth G], K [auth J], M [auth N], E [auth B], G [auth E], I [auth G], K [auth J], M [auth N], O [auth P], Q [auth R], S [auth T], U [auth W], W [auth Z]	Light-harvesting protein B-870 beta chain	chlorophyll binding binding bacteriochlorophyll binding tetrapyrrole binding cation binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction metabolic process cellular process generation of precursor metabolites and energy	cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular anatomical structure intracellular vesicle plasma membrane-derived chromatophore light-harvesting complex intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular anatomical structure intracellular vesicle plasma membrane-derived chromatophore light-harvesting complex intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle
D [auth A], F [auth D], H [auth F], J [auth I], L [auth K], D [auth A], F [auth D], H [auth F], J [auth I], L [auth K], N [auth O], P [auth Q], R [auth S], T [auth V], V [auth Y]	Light-harvesting protein B-870 alpha chain	chlorophyll binding binding bacteriochlorophyll binding tetrapyrrole binding cation binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction metabolic process cellular process generation of precursor metabolites and energy	membrane-bounded organelle intracellular organelle organelle envelope organelle inner membrane cellular anatomical structure intracellular anatomical structure organelle membrane organelle membrane cell periphery plasma membrane plasma membrane light-harvesting complex protein-containing complex intracellular vesicle membrane-bounded organelle intracellular organelle organelle envelope organelle inner membrane cellular anatomical structure intracellular anatomical structure organelle membrane organelle membrane cell periphery plasma membrane plasma membrane light-harvesting complex protein-containing complex intracellular vesicle plasma membrane-derived chromatophore light-harvesting complex intracellular membrane-bounded organelle cytoplasmic vesicle cytoplasm vesicle
C [auth H]	Photosynthetic reaction center H subunit	chlorophyll binding binding bacteriochlorophyll binding tetrapyrrole binding	photosynthesis photosynthesis, light reaction metabolic process cellular process generation of precursor metabolites and energy	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane intracellular membraneless organelle plasma membrane-derived chromatophore intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm photosynthetic membrane thylakoid membrane-bounded organelle plasma membrane light-harvesting complex intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane intracellular membraneless organelle plasma membrane-derived chromatophore intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm photosynthetic membrane thylakoid membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular vesicle light-harvesting complex intracellular membrane-bounded organelle cytoplasmic vesicle vesicle
B [auth M]	Reaction center protein M chain	chlorophyll binding binding bacteriochlorophyll binding tetrapyrrole binding cation binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain photosynthetic electron transport in photosystem II metabolic process cellular process generation of precursor metabolites and energy	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane intracellular membraneless organelle plasma membrane-derived chromatophore intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm photosynthetic membrane thylakoid membrane-bounded organelle plasma membrane light-harvesting complex intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane intracellular membraneless organelle plasma membrane-derived chromatophore intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm photosynthetic membrane thylakoid membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular vesicle light-harvesting complex intracellular membrane-bounded organelle cytoplasmic vesicle vesicle
A [auth L]	Reaction center protein L chain	chlorophyll binding binding bacteriochlorophyll binding tetrapyrrole binding cation binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain photosynthetic electron transport in photosystem II metabolic process cellular process generation of precursor metabolites and energy	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane intracellular membraneless organelle plasma membrane-derived chromatophore intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm photosynthetic membrane thylakoid membrane-bounded organelle plasma membrane light-harvesting complex intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane intracellular membraneless organelle plasma membrane-derived chromatophore intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm photosynthetic membrane thylakoid membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular vesicle light-harvesting complex intracellular membrane-bounded organelle cytoplasmic vesicle vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
X	IPR020169	Intrinsic membrane protein family, PufX	Family
E [auth B], G [auth E], I [auth G], K [auth J], M [auth N], E [auth B], G [auth E], I [auth G], K [auth J], M [auth N], O [auth P], Q [auth R], S [auth T], U [auth W], W [auth Z]	IPR000066	Antenna complex, alpha/beta subunit	Domain
E [auth B], G [auth E], I [auth G], K [auth J], M [auth N], E [auth B], G [auth E], I [auth G], K [auth J], M [auth N], O [auth P], Q [auth R], S [auth T], U [auth W], W [auth Z]	IPR023624	Antenna complex, beta domain superfamily	Homologous Superfamily
E [auth B], G [auth E], I [auth G], K [auth J], M [auth N], E [auth B], G [auth E], I [auth G], K [auth J], M [auth N], O [auth P], Q [auth R], S [auth T], U [auth W], W [auth Z]	IPR035889	Light-harvesting complex	Homologous Superfamily
E [auth B], G [auth E], I [auth G], K [auth J], M [auth N], E [auth B], G [auth E], I [auth G], K [auth J], M [auth N], O [auth P], Q [auth R], S [auth T], U [auth W], W [auth Z]	IPR023623	Antenna complex, beta subunit, conserved site	Conserved Site
E [auth B], G [auth E], I [auth G], K [auth J], M [auth N], E [auth B], G [auth E], I [auth G], K [auth J], M [auth N], O [auth P], Q [auth R], S [auth T], U [auth W], W [auth Z]	IPR002362	Light-harvesting protein B beta chain	Family
D [auth A], F [auth D], H [auth F], J [auth I], L [auth K], D [auth A], F [auth D], H [auth F], J [auth I], L [auth K], N [auth O], P [auth Q], R [auth S], T [auth V], V [auth Y]	IPR000066	Antenna complex, alpha/beta subunit	Domain
D [auth A], F [auth D], H [auth F], J [auth I], L [auth K], D [auth A], F [auth D], H [auth F], J [auth I], L [auth K], N [auth O], P [auth Q], R [auth S], T [auth V], V [auth Y]	IPR018332	Antenna complex, alpha subunit	Family
D [auth A], F [auth D], H [auth F], J [auth I], L [auth K], D [auth A], F [auth D], H [auth F], J [auth I], L [auth K], N [auth O], P [auth Q], R [auth S], T [auth V], V [auth Y]	IPR002361	Antenna complex, alpha subunit conserved site	Conserved Site
D [auth A], F [auth D], H [auth F], J [auth I], L [auth K], D [auth A], F [auth D], H [auth F], J [auth I], L [auth K], N [auth O], P [auth Q], R [auth S], T [auth V], V [auth Y]	IPR035889	Light-harvesting complex	Homologous Superfamily
C [auth H]	IPR014747	Bacterial photosynthetic reaction centre, H-chain, C-terminal	Homologous Superfamily
C [auth H]	IPR015810	Photosynthetic reaction centre, H subunit, N-terminal	Domain
C [auth H]	IPR005652	Photosynthetic reaction centre, H subunit	Family
C [auth H]	IPR037097	Photosynthetic reaction centre, H subunit, N-terminal domain superfamily	Homologous Superfamily
C [auth H]	IPR011033	PRC-barrel-like superfamily	Homologous Superfamily
C [auth H]	IPR027275	PRC-barrel domain	Domain
B [auth M]	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
B [auth M]	IPR005781	Photosynthetic reaction centre, M subunit	Family
B [auth M]	IPR000484	Photosynthetic reaction centre, L/M	Family
B [auth M]	IPR055265	Photosynthetic reaction centre, L/M, conserved site	Conserved Site
A [auth L]	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
A [auth L]	IPR000484	Photosynthetic reaction centre, L/M	Family
A [auth L]	IPR055265	Photosynthetic reaction centre, L/M, conserved site	Conserved Site
A [auth L]	IPR005871	Photosynthetic reaction centre, L subunit	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth L], B [auth M], C [auth H], D [auth A], E [auth B] A [auth L], B [auth M], C [auth H], D [auth A], E [auth B], F [auth D], G [auth E], H [auth F], I [auth G], J [auth I], K [auth J], L [auth K], M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth R], R [auth S], S [auth T], T [auth V], U [auth W], V [auth Y], W [auth Z], X	OPM	Transmembrane	Alpha-helical polytopic	Photosystems	Photosynthetic reaction centers from bacteria

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth L], B [auth M], C [auth H], D [auth A], E [auth B] A [auth L], B [auth M], C [auth H], D [auth A], E [auth B], F [auth D], G [auth E], H [auth F], I [auth G], J [auth I], K [auth J], L [auth K], M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth R], R [auth S], S [auth T], T [auth V], U [auth W], V [auth Y], W [auth Z], X	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth L], B [auth M], C [auth H], D [auth A], E [auth B] A [auth L], B [auth M], C [auth H], D [auth A], E [auth B], F [auth D], G [auth E], H [auth F], I [auth G], J [auth I], K [auth J], L [auth K], M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth R], R [auth S], S [auth T], T [auth V], U [auth W], V [auth Y], W [auth Z], X	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Light-Harvesting+Reaction Center Complexes	LH1-RC super complex

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D [auth A], F [auth D], H [auth F], J [auth I], L [auth K], D [auth A], F [auth D], H [auth F], J [auth I], L [auth K], N [auth O], P [auth Q], R [auth S], T [auth V], V [auth Y]	FME	Parent Component: MET : AA0021 , AA0566 : 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