1W5C | pdb_00001w5c

Photosystem II from Thermosynechococcus elongatus

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)
R [auth V]	d1w5cv_	Low resolution protein structures	Photosystems	Photosystems	Photosystems	Photosystem II	(Thermosynechococcus vestitus ) [TaxId: 146786 ],	SCOPe (2.08)
P [auth T]	d1w5ct_	Low resolution protein structures	Photosystems	Photosystems	Photosystems	Photosystem II	(Thermosynechococcus vestitus ) [TaxId: 146786 ],	SCOPe (2.08)
L	d1w5cl_	Low resolution protein structures	Photosystems	Photosystems	Photosystems	Photosystem II	(Thermosynechococcus vestitus ) [TaxId: 146786 ],	SCOPe (2.08)
F	d1w5cf_	Low resolution protein structures	Photosystems	Photosystems	Photosystems	Photosystem II	(Thermosynechococcus vestitus ) [TaxId: 146786 ],	SCOPe (2.08)
K	d1w5ck_	Low resolution protein structures	Photosystems	Photosystems	Photosystems	Photosystem II	(Thermosynechococcus vestitus ) [TaxId: 146786 ],	SCOPe (2.08)
E	d1w5ce_	Low resolution protein structures	Photosystems	Photosystems	Photosystems	Photosystem II	(Thermosynechococcus vestitus ) [TaxId: 146786 ],	SCOPe (2.08)
J	d1w5cj_	Low resolution protein structures	Photosystems	Photosystems	Photosystems	Photosystem II	(Thermosynechococcus vestitus ) [TaxId: 146786 ],	SCOPe (2.08)
D	d1w5cd_	Low resolution protein structures	Photosystems	Photosystems	Photosystems	Photosystem II	(Thermosynechococcus vestitus ) [TaxId: 146786 ],	SCOPe (2.08)
I	d1w5ci_	Low resolution protein structures	Photosystems	Photosystems	Photosystems	Photosystem II	(Thermosynechococcus vestitus ) [TaxId: 146786 ],	SCOPe (2.08)
C	d1w5cc_	Low resolution protein structures	Photosystems	Photosystems	Photosystems	Photosystem II	(Thermosynechococcus vestitus ) [TaxId: 146786 ],	SCOPe (2.08)
H	d1w5ch_	Low resolution protein structures	Photosystems	Photosystems	Photosystems	Photosystem II	(Thermosynechococcus vestitus ) [TaxId: 146786 ],	SCOPe (2.08)
B	d1w5cb_	Low resolution protein structures	Photosystems	Photosystems	Photosystems	Photosystem II	(Thermosynechococcus vestitus ) [TaxId: 146786 ],	SCOPe (2.08)
G	d1w5cg_	Low resolution protein structures	Photosystems	Photosystems	Photosystems	Photosystem II	(Thermosynechococcus vestitus ) [TaxId: 146786 ],	SCOPe (2.08)
A	d1w5ca_	Low resolution protein structures	Photosystems	Photosystems	Photosystems	Photosystem II	(Thermosynechococcus vestitus ) [TaxId: 146786 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
R [auth V]	SCOP2B Superfamily	Cytochrome c	8036565	3000815	SCOP2B (2022-06-29)
P [auth T]	SCOP2B Superfamily	Cytochrome c	8036565	3000815	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Cytochrome b559 subunits	8032752	3001602	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cytochrome b559 subunits	8032752	3001602	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Cytochrome b559 subunits	8032749	3001602	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cytochrome b559 subunits	8032749	3001602	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Bacterial photosystem II reaction centre, L and M subunits	8032750	3000736	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Bacterial photosystem II reaction centre, L and M subunits	8032750	3000736	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Photosystem II antenna protein-like	8032746	3001674	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Photosystem II antenna protein-like	8032746	3001674	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Photosystem II antenna protein-like	8032743	3001674	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Photosystem II antenna protein-like	8032743	3001674	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Bacterial photosystem II reaction centre, L and M subunits	8032741	3000736	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bacterial photosystem II reaction centre, L and M subunits	8032741	3000736	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)
R [auth V]	tRNA-synt_1b	e1w5cV1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: tRNA-synt_1b	ECOD (v294.1)
P [auth T]	YbeY	e1w5cT1	A: a/b three-layered sandwiches	X: Globin-like	H: Ring-building motif I in type III secretion system	T: Ring-building motif I in type III secretion system	F: YbeY	ECOD (v294.1)
L	tRNA-synt_1b	e1w5cL1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: tRNA-synt_1b	ECOD (v294.1)
F	tRNA-synt_1b	e1w5cF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: tRNA-synt_1b	ECOD (v294.1)
K	tRNA-synt_1b	e1w5cK1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: tRNA-synt_1b	ECOD (v294.1)
E	YbeY	e1w5cE1	A: a/b three-layered sandwiches	X: Globin-like	H: Ring-building motif I in type III secretion system	T: Ring-building motif I in type III secretion system	F: YbeY	ECOD (v294.1)
J	tRNA-synt_1b	e1w5cJ1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: tRNA-synt_1b	ECOD (v294.1)
D	YbeY	e1w5cD1	A: a/b three-layered sandwiches	X: Globin-like	H: Ring-building motif I in type III secretion system	T: Ring-building motif I in type III secretion system	F: YbeY	ECOD (v294.1)
I	TPR_2, TPR_P4H	e1w5cI1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: ARM repeat	T: ARM repeat	F: TPR_2, TPR_P4H	ECOD (v294.1)
C	YbeY	e1w5cC1	A: a/b three-layered sandwiches	X: Globin-like	H: Ring-building motif I in type III secretion system	T: Ring-building motif I in type III secretion system	F: YbeY	ECOD (v294.1)
H	TPR_2, TPR_P4H	e1w5cH1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: ARM repeat	T: ARM repeat	F: TPR_2, TPR_P4H	ECOD (v294.1)
B	TPR_2, TPR_P4H	e1w5cB1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: ARM repeat	T: ARM repeat	F: TPR_2, TPR_P4H	ECOD (v294.1)
G	tRNA-synt_1b	e1w5cG1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: tRNA-synt_1b	ECOD (v294.1)
A	YbeY	e1w5cA1	A: a/b three-layered sandwiches	X: Globin-like	H: Ring-building motif I in type III secretion system	T: Ring-building motif I in type III secretion system	F: YbeY	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
R [auth V]	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
P [auth T]	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
K	1.20.5.860	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Photosystem II cytochrome b559, alpha subunit	CATH (4.3.0)
E	1.20.5.860	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Photosystem II cytochrome b559, alpha subunit	CATH (4.3.0)
I	1.10.10.670	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	photosystem ii from thermosynechococcus elongatus	CATH (4.3.0)
C	1.10.10.670	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	photosystem ii from thermosynechococcus elongatus	CATH (4.3.0)
H	3.10.680.10	Alpha Beta	Roll	Photosystem II CP47 reaction center protein	Photosystem II CP47 reaction center protein	CATH (4.3.0)
B	3.10.680.10	Alpha Beta	Roll	Photosystem II CP47 reaction center protein	Photosystem II CP47 reaction center protein	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, K	PF00284	Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit (Cytochrom_B559a)	Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit	-	Family
D, J	PF00124	Photosynthetic reaction centre protein (Photo_RC)	Photosynthetic reaction centre protein	-	Family
C, I	PF00421	Photosystem II protein (PSII)	Photosystem II protein	-	Family
A, G	PF00124	Photosynthetic reaction centre protein (Photo_RC)	Photosynthetic reaction centre protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
P [auth T], R [auth V]	CYTOCHROME C-550	binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction metabolic process cellular process generation of precursor metabolites and energy cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid plasma membrane-derived chromatophore membrane protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid plasma membrane-derived chromatophore membrane plasma membrane plasma membrane-derived chromatophore thylakoid membrane cell periphery plasma membrane-derived thylakoid membrane plasma membrane region bacterial thylakoid cytoplasm
O [auth S], Q [auth U]	PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN	-	-	-
M [auth O], N [auth P]	PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE	-	-	-
F, L	CYTOCHROME B559 BETA SUBUNIT	binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid plasma membrane-derived chromatophore membrane plasma membrane plasma membrane-derived chromatophore thylakoid membrane cell periphery plasma membrane-derived thylakoid membrane plasma membrane region bacterial thylakoid cytoplasm
E, K	CYTOCHROME B559 ALPHA SUBUNIT	binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle photosystem II reaction center intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid plasma membrane-derived chromatophore membrane plasma membrane plasma membrane-derived chromatophore thylakoid membrane cell periphery plasma membrane-derived thylakoid membrane plasma membrane region bacterial thylakoid cytoplasm
D, J	PHOTOSYSTEM II REACTION CENTER D2 PROTEIN	oxidoreductase activity oxygen evolving activity catalytic activity chlorophyll binding binding tetrapyrrole binding electron transfer activity cation binding transition metal ion binding iron ion 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	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid plasma membrane-derived chromatophore membrane protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid plasma membrane-derived chromatophore membrane plasma membrane plasma membrane-derived chromatophore thylakoid membrane cell periphery plasma membrane-derived thylakoid membrane plasma membrane region bacterial thylakoid cytoplasm
C, I	PHOTOSYSTEM II CP43 PROTEIN	chlorophyll binding 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	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid plasma membrane-derived chromatophore membrane protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid plasma membrane-derived chromatophore membrane plasma membrane plasma membrane-derived chromatophore thylakoid membrane cell periphery plasma membrane-derived thylakoid membrane plasma membrane region bacterial thylakoid cytoplasm
B, H	PHOTOSYSTEM II CORE LIGHT HARVESTING PROTEIN	chlorophyll binding binding tetrapyrrole 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	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid plasma membrane-derived chromatophore membrane protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid plasma membrane-derived chromatophore membrane plasma membrane plasma membrane-derived chromatophore thylakoid membrane cell periphery plasma membrane-derived thylakoid membrane plasma membrane region bacterial thylakoid cytoplasm
S [auth X], T [auth Y]	UNASSIGNED SUBUNITS	-	-	-
A, G	PHOTOSYSTEM Q(B) PROTEIN 1	oxidoreductase activity oxygen evolving activity catalytic activity chlorophyll binding binding tetrapyrrole binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor oxidoreductase activity, acting on diphenols and related substances as donors oxidoreductase activity oxygen evolving activity catalytic activity chlorophyll binding binding tetrapyrrole binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor oxidoreductase activity, acting on diphenols and related substances as donors electron transfer activity	response to stimulus response to chemical response to stress response to herbicide response to toxic substance 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	protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid plasma membrane-derived chromatophore membrane protein-containing complex photosystem intracellular anatomical structure photosystem II membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane thylakoid plasma membrane-derived chromatophore membrane plasma membrane plasma membrane-derived chromatophore thylakoid membrane cell periphery plasma membrane-derived thylakoid membrane plasma membrane region bacterial thylakoid cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
P [auth T], R [auth V]	IPR017851	Photosystem II extrinsic protein V, cytochrome c-550 precursor	Family
P [auth T], R [auth V]	IPR016003	Photosystem II extrinsic protein V, cytochrome c-550 precursor-like	Family
P [auth T], R [auth V]	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
P [auth T], R [auth V]	IPR009056	Cytochrome c-like domain	Domain
P [auth T], R [auth V]	IPR029490	Cytochrome c-550 domain	Domain
F, L	IPR006241	Photosystem II cytochrome b559, beta subunit	Family
F, L	IPR013081	Photosystem II cytochrome b559, N-terminal	Domain
F, L	IPR006216	Photosystem II cytochrome b559, conserved site	Conserved Site
E, K	IPR013081	Photosystem II cytochrome b559, N-terminal	Domain
E, K	IPR006217	Photosystem II cytochrome b559, alpha subunit	Family
E, K	IPR013082	Photosystem II cytochrome b559, alpha subunit, lumenal region	Domain
E, K	IPR037025	Photosystem II cytochrome b559, alpha subunit superfamily	Homologous Superfamily
E, K	IPR006216	Photosystem II cytochrome b559, conserved site	Conserved Site
D, J	IPR005868	Photosystem II D2	Family
D, J	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
D, J	IPR000484	Photosynthetic reaction centre, L/M	Family
D, J	IPR055265	Photosynthetic reaction centre, L/M, conserved site	Conserved Site
D, J	IPR055266	Photosystem II protein D1/D2	Family
C, I	IPR036001	Photosystem antenna protein-like superfamily	Homologous Superfamily
C, I	IPR000932	Photosystem antenna protein-like	Family
C, I	IPR005869	Photosystem II CP43 reaction centre protein	Family
C, I	IPR044900	Photosystem II CP43 reaction centre protein superfamily	Homologous Superfamily
B, H	IPR036001	Photosystem antenna protein-like superfamily	Homologous Superfamily
B, H	IPR000932	Photosystem antenna protein-like	Family
B, H	IPR017486	Photosystem II CP47 reaction centre protein	Family
A, G	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
A, G	IPR005867	Photosystem II protein D1	Family
A, G	IPR000484	Photosynthetic reaction centre, L/M	Family
A, G	IPR055265	Photosynthetic reaction centre, L/M, conserved site	Conserved Site
A, G	IPR055266	Photosystem II protein D1/D2	Family