6FTL | pdb_00006ftl

Rubisco from Skeletonema marinoi

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H [auth L]	d6ftll_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Skeletonema marinoi ) [TaxId: 267567 ],	SCOPe (2.08)
F [auth K]	d6ftlk_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Skeletonema marinoi ) [TaxId: 267567 ],	SCOPe (2.08)
D [auth J]	d6ftlj_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Skeletonema marinoi ) [TaxId: 267567 ],	SCOPe (2.08)
B [auth I]	d6ftli_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Skeletonema marinoi ) [TaxId: 267567 ],	SCOPe (2.08)
G	d6ftlg2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Skeletonema marinoi ) [TaxId: 267567 ],	SCOPe (2.08)
G	d6ftlg1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Skeletonema marinoi ) [TaxId: 267567 ],	SCOPe (2.08)
E	d6ftle2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Skeletonema marinoi ) [TaxId: 267567 ],	SCOPe (2.08)
E	d6ftle1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Skeletonema marinoi ) [TaxId: 267567 ],	SCOPe (2.08)
C	d6ftlc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Skeletonema marinoi ) [TaxId: 267567 ],	SCOPe (2.08)
C	d6ftlc1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Skeletonema marinoi ) [TaxId: 267567 ],	SCOPe (2.08)
A	d6ftla2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Skeletonema marinoi ) [TaxId: 267567 ],	SCOPe (2.08)
A	d6ftla1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Skeletonema marinoi ) [TaxId: 267567 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H [auth L]	SCOP2B Superfamily	RuBisCO, small subunit	8095057	3001622	SCOP2B (2022-06-29)
F [auth K]	SCOP2B Superfamily	RuBisCO, small subunit	8095057	3001622	SCOP2B (2022-06-29)
D [auth J]	SCOP2B Superfamily	RuBisCO, small subunit	8095057	3001622	SCOP2B (2022-06-29)
B [auth I]	SCOP2 Family	RuBisCO, small subunit	8095056	4001455	SCOP2 (2022-06-29)
B [auth I]	SCOP2 Superfamily	RuBisCO, small subunit	8095057	3001622	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)
H [auth L]	RuBisCO_small	e6ftlL1	A: a+b two layers	X: Reverse ferredoxin	H: RuBisCO, small subunit (From Topology)	T: RuBisCO, small subunit	F: RuBisCO_small	ECOD (1.6)
F [auth K]	RuBisCO_small	e6ftlK1	A: a+b two layers	X: Reverse ferredoxin	H: RuBisCO, small subunit (From Topology)	T: RuBisCO, small subunit	F: RuBisCO_small	ECOD (1.6)
D [auth J]	RuBisCO_small	e6ftlJ1	A: a+b two layers	X: Reverse ferredoxin	H: RuBisCO, small subunit (From Topology)	T: RuBisCO, small subunit	F: RuBisCO_small	ECOD (1.6)
B [auth I]	RuBisCO_small	e6ftlI1	A: a+b two layers	X: Reverse ferredoxin	H: RuBisCO, small subunit (From Topology)	T: RuBisCO, small subunit	F: RuBisCO_small	ECOD (1.6)
G	RuBisCO_large_N	e6ftlG1	A: a+b two layers	X: Alpha-beta plaits	H: RuBisCO, large subunit, small (N-terminal) domain (From Topology)	T: RuBisCO, large subunit, small (N-terminal) domain	F: RuBisCO_large_N	ECOD (1.6)
G	RuBisCO_large	e6ftlG2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
E	RuBisCO_large_N	e6ftlE2	A: a+b two layers	X: Alpha-beta plaits	H: RuBisCO, large subunit, small (N-terminal) domain (From Topology)	T: RuBisCO, large subunit, small (N-terminal) domain	F: RuBisCO_large_N	ECOD (1.6)
E	RuBisCO_large	e6ftlE1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
C	RuBisCO_large_N	e6ftlC2	A: a+b two layers	X: Alpha-beta plaits	H: RuBisCO, large subunit, small (N-terminal) domain (From Topology)	T: RuBisCO, large subunit, small (N-terminal) domain	F: RuBisCO_large_N	ECOD (1.6)
C	RuBisCO_large	e6ftlC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
A	RuBisCO_large_N	e6ftlA1	A: a+b two layers	X: Alpha-beta plaits	H: RuBisCO, large subunit, small (N-terminal) domain (From Topology)	T: RuBisCO, large subunit, small (N-terminal) domain	F: RuBisCO_large_N	ECOD (1.6)
A	RuBisCO_large	e6ftlA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth L]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
F [auth K]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
D [auth J]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
B [auth I]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
G	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
G	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
E	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
E	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
C	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
C	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
A	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
A	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth I], D [auth J], F [auth K], H [auth L]	PF00101	Ribulose bisphosphate carboxylase, small chain (RuBisCO_small)	Ribulose bisphosphate carboxylase, small chain		Domain
A, C, E, G	PF02788	Ribulose bisphosphate carboxylase large chain, N-terminal domain (RuBisCO_large_N)	Ribulose bisphosphate carboxylase large chain, N-terminal domain	The N-terminal domain of RuBisCO large chain adopts a ferredoxin-like fold.	Domain
A, C, E, G	PF00016	Ribulose bisphosphate carboxylase large chain, catalytic domain (RuBisCO_large)	Ribulose bisphosphate carboxylase large chain, catalytic domain	The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth I], D [auth J], F [auth K], H [auth L]	Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit	ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process cellular process carbon fixation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast
A, C, E, G	Ribulose bisphosphate carboxylase large chain	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding monooxygenase activity oxidoreductase activity catalytic activity ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity carbon-carbon lyase activity	carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process cellular process carbon fixation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth I], D [auth J], F [auth K], H [auth L]	IPR036385	Ribulose bisphosphate carboxylase, small subunit superfamily	Homologous Superfamily
B [auth I], D [auth J], F [auth K], H [auth L]	IPR024681	Ribulose bisphosphate carboxylase, small subunit	Family
B [auth I], D [auth J], F [auth K], H [auth L]	IPR000894	Ribulose bisphosphate carboxylase small subunit, domain	Domain
A, C, E, G	IPR020888	Ribulose bisphosphate carboxylase large subunit, type I	Family
A, C, E, G	IPR036376	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily	Homologous Superfamily
A, C, E, G	IPR020878	Ribulose bisphosphate carboxylase, large chain, active site	Active Site
A, C, E, G	IPR000685	Ribulose bisphosphate carboxylase, large subunit, C-terminal	Domain
A, C, E, G	IPR033966	RuBisCO	Family
A, C, E, G	IPR036422	RuBisCO large subunit, N-terminal domain superfamily	Homologous Superfamily
A, C, E, G	IPR017443	Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C, E, G	HLU	Parent Component: LEU
A, C, E, G	HYP	Parent Component: PRO RESID: AA0030 PSI-MOD : 4-hydroxy-L-proline MOD:00039
A, C, E, G	KCX	Parent Component: LYS RESID: AA0030
A, C, E, G	LOH	RESID: AA0030
A, C, E, G	LYO	Parent Component: LYS RESID: AA0030
A, C, E, G	M3L	Parent Component: LYS RESID: AA0030 , AA0074 PSI-MOD : 4-hydroxy-L-proline MOD:00039 , N6,N6,N6-trimethyl-L-lysine MOD:00083

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.