3WQP | pdb_00003wqp

Crystal structure of Rubisco T289D mutant from Thermococcus kodakarensis

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)
J	d3wqpj2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
J	d3wqpj1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
I	d3wqpi2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
I	d3wqpi1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
H	d3wqph2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
H	d3wqph1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
G	d3wqpg2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
G	d3wqpg1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
F	d3wqpf2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
F	d3wqpf1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
E	d3wqpe2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
E	d3wqpe1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
D	d3wqpd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
D	d3wqpd1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
C	d3wqpc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
C	d3wqpc1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
B	d3wqpb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
B	d3wqpb1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
A	d3wqpa2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)
A	d3wqpa1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thermococcus kodakarensis KOD1 ) [TaxId: 69014 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035844	3001258	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	RuBisCo, C-terminal domain	8035841	3000552	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035844	3001258	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	RuBisCo, C-terminal domain	8035841	3000552	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035844	3001258	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RuBisCo, C-terminal domain	8035841	3000552	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035844	3001258	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RuBisCo, C-terminal domain	8035841	3000552	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RuBisCo, C-terminal domain	8035841	3000552	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035844	3001258	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RuBisCo, C-terminal domain	8035841	3000552	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035844	3001258	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RuBisCo, C-terminal domain	8035841	3000552	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035844	3001258	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RuBisCo, C-terminal domain	8035841	3000552	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035844	3001258	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035844	3001258	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RuBisCo, C-terminal domain	8035841	3000552	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RuBisCO, large subunit, small (N-terminal) domain	8035844	3001258	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RuBisCo, C-terminal domain	8035841	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)
J	Beta-Casp	e3wqpJ1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
I	Beta-Casp	e3wqpI1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
H	Beta-Casp	e3wqpH1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
G	Beta-Casp	e3wqpG1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
F	Beta-Casp	e3wqpF1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
E	Beta-Casp	e3wqpE1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
D	Beta-Casp	e3wqpD1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
C	Beta-Casp	e3wqpC1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)
B	RuBisCO_large	e3wqpB1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: RuBisCO_large	ECOD (v294.1)
A	Beta-Casp	e3wqpA1	A: a/b three-layered sandwiches	X: Glycosyl hydrolase domain-like	H: Glycoside hydrolase family 127 middle domain-related	T: Glycoside hydrolase family 127 middle domain-related	F: Beta-Casp	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
J	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
I	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
I	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
H	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
H	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
G	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
G	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
F	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
F	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
E	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
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	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	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, C, D, E A, B, C, D, E, F, G, H, I, J	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, C, D, E A, B, C, D, E, F, G, H, I, J	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, E A, B, C, D, E, F, G, H, I, J	IPR036376	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR000685	Ribulose bisphosphate carboxylase, large subunit, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR033966	RuBisCO	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR036422	RuBisCO large subunit, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR017712	Ribulose bisphosphate carboxylase, type III	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR017443	Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal	Domain