Annotations: 1YKW

Crystal Structure of a Novel RuBisCO-Like Protein from the Green Sulfur Bacterium Chlorobium tepidum

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1ykwb1	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	(Chlorobaculum tepidum ) [TaxId: 1097 ],	SCOPe (2.08)
B	d1ykwb2	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	(Chlorobaculum tepidum ) [TaxId: 1097 ],	SCOPe (2.08)
A	d1ykwa1	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	(Chlorobaculum tepidum ) [TaxId: 1097 ],	SCOPe (2.08)
A	d1ykwa2	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	(Chlorobaculum tepidum ) [TaxId: 1097 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	RuBisCo, C-terminal domain	8034672	3000552	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8034674	3001258	SCOP2B (2022-06-29)
A	SCOP2 Family	RuBisCo, large subunit, C-terminal domain	8022292	4003287	SCOP2 (2022-06-29)
A	SCOP2 Family	Ribulose 1, 5-bisphosphate carboxylase-oxygenase	8022294	4001311	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RuBisCo, C-terminal domain	8034672	3000552	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8034674	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)
B	RNase_P_Rpp14	e1ykwB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)
B	DUF711	e1ykwB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
A	RuBisCO_large_N	e1ykwA1	A: a+b two layers	X: Alpha-beta plaits	H: RuBisCO, large subunit, small (N-terminal) domain	T: RuBisCO, large subunit, small (N-terminal) domain	F: RuBisCO_large_N	ECOD (v294.1)
A	RuBisCO_large	e1ykwA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: RuBisCO_large	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
B	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
A, B	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, B	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
A, B	RuBisCO-like protein	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	metabolic process cellular process carbon fixation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036376	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR000685	Ribulose bisphosphate carboxylase, large subunit, C-terminal	Domain
A, B	IPR033966	RuBisCO	Family
A, B	IPR036422	RuBisCO large subunit, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR017443	Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal	Domain

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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.