1WDD | pdb_00001wdd

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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
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)
A	SCOP2 Family	RuBisCo, large subunit, C-terminal domain	8031043	4003287	SCOP2 (2022-06-29)
A	SCOP2 Family	Ribulose 1, 5-bisphosphate carboxylase-oxygenase	8031045	4001311	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RuBisCo, C-terminal domain	8043421	3000552	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8043423	3001258	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)
D [auth W]		e1wddW1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
B [auth S]		e1wddS1	A: Reverse ferredoxin	X: RuBisCO, small subunit	H: RuBisCO, small subunit	T: RuBisCO_small	F:	ECOD (20:10:01)
C [auth E]		e1wddE1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Fer4,DUF3470	F:	ECOD (20:10:01)
C [auth E]		e1wddE2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Epimerase	F:	ECOD (20:10:01)
A		e1wddA1	A: Alpha-beta plaits	X: Probable ACP-binding domain of malonyl-CoA ACP transacylase	H: Probable ACP-binding domain of malonyl-CoA ACP transacylase	T:	F:	ECOD (20:10:01)
A		e1wddA2	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: RuBisCO_large	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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 S], D [auth W]	PF00101	Ribulose bisphosphate carboxylase, small chain (RuBisCO_small)	Ribulose bisphosphate carboxylase, small chain		Domain
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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	metabolic compound salvage biosynthetic process metabolic process cellular process photorespiration carbohydrate metabolic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process carbon fixation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast
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 nucleotide binding heterocyclic compound 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 nucleotide binding heterocyclic compound binding monooxygenase activity oxidoreductase activity	metabolic compound salvage biosynthetic process metabolic process cellular process photorespiration carbohydrate metabolic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process carbon fixation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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

Protein Modification Annotation

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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.