2CXE | pdb_00002cxe

Crystal structure of octameric ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Pyrococcus horikoshii OT3 (form-2 crystal)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d2cxed1	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	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
D	d2cxed2	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
C	d2cxec1	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	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
C	d2cxec2	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
B	d2cxeb1	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	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
B	d2cxeb2	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
A	d2cxea1	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	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
A	d2cxea2	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Pyrococcus horikoshii OT3 ) [TaxId: 70601 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8039597	3001258	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RuBisCo, C-terminal domain	8039595	3000552	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8039597	3001258	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RuBisCo, C-terminal domain	8039595	3000552	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RuBisCo, C-terminal domain	8039595	3000552	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8039597	3001258	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8039597	3001258	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RuBisCo, C-terminal domain	8039595	3000552	SCOP2B (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	RNase_P_Rpp14	e2cxeD1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
D	DUF711	e2cxeD2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (develop294)
C	RNase_P_Rpp14	e2cxeC1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
C	DUF711	e2cxeC2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (develop294)
B	RNase_P_Rpp14	e2cxeB1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
B	DUF711	e2cxeB2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (develop294)
A	RNase_P_Rpp14	e2cxeA1	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
A	DUF711	e2cxeA2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
D	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)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Ribulose bisphosphate carboxylase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding oxidoreductase activity catalytic activity ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity carbon-carbon lyase activity	ribose phosphate metabolic process ribonucleotide catabolic process catabolic process organophosphate catabolic process carbohydrate derivative metabolic process nucleoside phosphate catabolic process AMP metabolic process purine ribonucleoside monophosphate catabolic process purine nucleoside monophosphate catabolic process nucleobase-containing compound metabolic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine nucleoside monophosphate metabolic process ribose phosphate metabolic process ribonucleotide catabolic process catabolic process organophosphate catabolic process carbohydrate derivative metabolic process nucleoside phosphate catabolic process AMP metabolic process purine ribonucleoside monophosphate catabolic process purine nucleoside monophosphate catabolic process nucleobase-containing compound metabolic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine nucleoside monophosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process ribonucleoside monophosphate catabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside monophosphate metabolic process nucleotide catabolic process nucleoside phosphate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process nucleoside monophosphate catabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process organophosphate metabolic process AMP catabolic process metabolic process cellular process purine ribonucleotide metabolic process carbon fixation	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036376	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR000685	Ribulose bisphosphate carboxylase, large subunit, C-terminal	Domain
A, B, C, D	IPR033966	RuBisCO	Family
A, B, C, D	IPR036422	RuBisCO large subunit, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR017712	Ribulose bisphosphate carboxylase, type III	Family
A, B, C, D	IPR017443	Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal	Domain

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.