1SVD

The structure of Halothiobacillus neapolitanus RuBisCo

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

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1svda1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	Ribulose 1,5-bisphosphate carboxylase-oxygenase	(Halothiobacillus neapolitanus ) [TaxId: 927 ],	SCOPe (2.08)
A	d1svda2	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	Ribulose 1,5-bisphosphate carboxylase-oxygenase	Ribulose 1,5-bisphosphate carboxylase-oxygenase	(Halothiobacillus neapolitanus ) [TaxId: 927 ],	SCOPe (2.08)
B [auth M]	d1svdm1	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	Ribulose 1,5-bisphosphate carboxylase-oxygenase	(Halothiobacillus neapolitanus ) [TaxId: 927 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Ribulose 1 5-bisphosphate carboxylase-oxygenase	8020019	4001311	SCOP2 (2022-06-29)
A	SCOP2 Family	RuBisCo large subunit C-terminal domain	8020018	4003287	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RuBisCO large subunit small (N-terminal) domain	8032399	3001258	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RuBisCo C-terminal domain	8032398	3000552	SCOP2 (2022-06-29)
B [auth M]	SCOP2 Family	RuBisCO small subunit	8020022	4001455	SCOP2 (2022-06-29)
B [auth M]	SCOP2 Superfamily	RuBisCO small subunit	8032402	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)
A	RuBisCO_large_N	e1svdA1	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	e1svdA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: RuBisCO_large	ECOD (1.6)
B [auth M]	RuBisCO_small	e1svdM1	A: a+b two layers	X: Reverse ferredoxin	H: RuBisCO, small subunit (From Topology)	T: RuBisCO, small subunit	F: RuBisCO_small	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
B [auth M]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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
B [auth M]	PF00101	Ribulose bisphosphate carboxylase, small chain (RuBisCO_small)	Ribulose bisphosphate carboxylase, small chain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit	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 photosynthesis carbohydrate biosynthetic process cellular metabolic process photosynthesis, dark reaction primary metabolic process organic substance metabolic process biosynthetic process reductive pentose-phosphate cycle organic substance biosynthetic process metabolic process cellular process carbon fixation	intracellular organelle bacterial microcompartment intracellular anatomical structure organelle carboxysome intracellular non-membrane-bounded organelle cellular anatomical entity non-membrane-bounded organelle
B [auth M]	Ribulose bisphosphate carboxylase small chain	ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	carbohydrate metabolic process photosynthesis carbohydrate biosynthetic process cellular metabolic process photosynthesis, dark reaction primary metabolic process organic substance metabolic process biosynthetic process reductive pentose-phosphate cycle organic substance biosynthetic process metabolic process cellular process carbon fixation	intracellular organelle bacterial microcompartment intracellular anatomical structure organelle carboxysome intracellular non-membrane-bounded organelle cellular anatomical entity non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.