1WDD

Crystal Structure of Activated Rice Rubisco Complexed with 2-Carboxyarabinitol-1,5-bisphosphate

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)
A	d1wdda1	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	(Oryza sativa Japonica Group ) [TaxId: 39947 ],	SCOPe (2.08)
A	d1wdda2	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	(Oryza sativa Japonica Group ) [TaxId: 39947 ],	SCOPe (2.08)
C [auth E]	d1wdde1	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	(Oryza sativa Japonica Group ) [TaxId: 39947 ],	SCOPe (2.08)
C [auth E]	d1wdde2	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	(Oryza sativa Japonica Group ) [TaxId: 39947 ],	SCOPe (2.08)
D [auth W]	d1wddw_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	Ribulose 1,5-bisphosphate carboxylase-oxygenase	(Oryza sativa Japonica Group ) [TaxId: 39947 ],	SCOPe (2.08)
B [auth S]	d1wdds_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	RuBisCO, small subunit	Ribulose 1,5-bisphosphate carboxylase-oxygenase	(Oryza sativa Japonica Group ) [TaxId: 39947 ],	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	8031045	4001311	SCOP2 (2022-06-29)
A	SCOP2 Family	RuBisCo large subunit C-terminal domain	8031043	4003287	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RuBisCO large subunit small (N-terminal) domain	8043423	3001258	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RuBisCo C-terminal domain	8043421	3000552	SCOP2 (2022-06-29)
C [auth E]	SCOP2B Superfamily	RuBisCO large subunit small (N-terminal) domain	8043423	3001258	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	RuBisCo C-terminal domain	8043421	3000552	SCOP2B (2022-06-29)
D [auth W]	SCOP2B Superfamily	RuBisCO small subunit	8043428	3001622	SCOP2B (2022-06-29)
B [auth S]	SCOP2 Family	RuBisCO small subunit	8031050	4001455	SCOP2 (2022-06-29)
B [auth S]	SCOP2 Superfamily	RuBisCO small subunit	8043428	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	PF02788	e1wddA1	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: PF02788	ECOD (1.6)
A	PF00016	e1wddA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00016	ECOD (1.6)
C [auth E]	PF02788	e1wddE1	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: PF02788	ECOD (1.6)
C [auth E]	PF00016	e1wddE2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00016	ECOD (1.6)
D [auth W]	PF00101	e1wddW1	A: a+b two layers	X: Reverse ferredoxin	H: RuBisCO, small subunit (From Topology)	T: RuBisCO, small subunit	F: PF00101	ECOD (1.6)
B [auth S]	PF00101	e1wddS1	A: a+b two layers	X: Reverse ferredoxin	H: RuBisCO, small subunit (From Topology)	T: RuBisCO, small subunit	F: PF00101	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)
C [auth E]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
C [auth E]	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
D [auth W]	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 S]	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, C [auth E]	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 [auth E]	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 S], D [auth W]	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, C [auth E]	Ribulose bisphosphate carboxylase large chain	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity nucleoside phosphate binding organic cyclic compound binding nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding monooxygenase activity oxidoreductase activity	cellular metabolic process metabolic process cellular process cellular metabolic compound salvage photorespiration carbohydrate metabolic process photosynthesis carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process organic substance metabolic process biosynthetic process reductive pentose-phosphate cycle organic substance biosynthetic process cellular metabolic process metabolic process cellular process cellular metabolic compound salvage photorespiration carbohydrate metabolic process photosynthesis carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process organic substance metabolic process biosynthetic process reductive pentose-phosphate cycle organic substance biosynthetic process carbon fixation	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast
B [auth S], D [auth W]	Ribulose bisphosphate carboxylase small chain C	ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	cellular metabolic process metabolic process cellular process cellular metabolic compound salvage photorespiration carbohydrate metabolic process photosynthesis carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process organic substance metabolic process biosynthetic process reductive pentose-phosphate cycle organic substance biosynthetic process cellular metabolic process metabolic process cellular process cellular metabolic compound salvage photorespiration carbohydrate metabolic process photosynthesis carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process organic substance metabolic process biosynthetic process reductive pentose-phosphate cycle organic substance biosynthetic process carbon fixation	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth E]	IPR020888	Ribulose bisphosphate carboxylase large subunit, type I	Family
A, C [auth E]	IPR036376	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily	Homologous Superfamily
A, C [auth E]	IPR020878	Ribulose bisphosphate carboxylase, large chain, active site	Active Site
A, C [auth E]	IPR000685	Ribulose bisphosphate carboxylase, large subunit, C-terminal	Domain
A, C [auth E]	IPR033966	RuBisCO	Family
A, C [auth E]	IPR017443	Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal	Domain
A, C [auth E]	IPR036422	RuBisCO large subunit, N-terminal domain superfamily	Homologous Superfamily
B [auth S], D [auth W]	IPR024680	Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal	Domain
B [auth S], D [auth W]	IPR036385	Ribulose bisphosphate carboxylase, small subunit superfamily	Homologous Superfamily
B [auth S], D [auth W]	IPR024681	Ribulose bisphosphate carboxylase, small subunit	Family
B [auth S], D [auth W]	IPR000894	Ribulose bisphosphate carboxylase small subunit, domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C [auth E]	KCX	Parent Component: LYS
B [auth S], D [auth W]	MME	Parent Component: MET RESID: AA0064 PSI-MOD : N-methyl-L-methionine MOD:00073

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.