5N9Z | pdb_00005n9z

Rubisco from Thalassiosira hyalina

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
P [auth L]	d5n9zl_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
N [auth K]	d5n9zk_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
L [auth J]	d5n9zj_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
J [auth P]	d5n9zp_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
H [auth M]	d5n9zm_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
F [auth N]	d5n9zn_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
D [auth O]	d5n9zo_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
B [auth I]	d5n9zi_	Alpha and beta proteins (a+b)	RuBisCO, small subunit	RuBisCO, small subunit	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
O [auth G]	d5n9zg2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
O [auth G]	d5n9zg1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
M [auth E]	d5n9ze2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
M [auth E]	d5n9ze1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
K [auth C]	d5n9zc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
K [auth C]	d5n9zc1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
I [auth B]	d5n9zb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
I [auth B]	d5n9zb1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
G [auth D]	d5n9zd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
G [auth D]	d5n9zd1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
E [auth F]	d5n9zf2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
E [auth F]	d5n9zf1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
C [auth H]	d5n9zh2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
C [auth H]	d5n9zh1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
A	d5n9za2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	RuBisCo, C-terminal domain	RuBisCo, large subunit, C-terminal domain	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)
A	d5n9za1	Alpha and beta proteins (a+b)	Ferredoxin-like	RuBisCO, large subunit, small (N-terminal) domain	automated matches	automated matches	(Thalassiosira hyalina ) [TaxId: 1234817 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
P [auth L]	SCOP2B Superfamily	RuBisCO, small subunit	8094981	3001622	SCOP2B (2022-06-29)
N [auth K]	SCOP2B Superfamily	RuBisCO, small subunit	8094981	3001622	SCOP2B (2022-06-29)
L [auth J]	SCOP2B Superfamily	RuBisCO, small subunit	8094981	3001622	SCOP2B (2022-06-29)
J [auth P]	SCOP2B Superfamily	RuBisCO, small subunit	8094981	3001622	SCOP2B (2022-06-29)
H [auth M]	SCOP2B Superfamily	RuBisCO, small subunit	8094981	3001622	SCOP2B (2022-06-29)
F [auth N]	SCOP2B Superfamily	RuBisCO, small subunit	8094981	3001622	SCOP2B (2022-06-29)
D [auth O]	SCOP2 Family	RuBisCO, small subunit	8094980	4001455	SCOP2 (2022-06-29)
D [auth O]	SCOP2 Superfamily	RuBisCO, small subunit	8094981	3001622	SCOP2 (2022-06-29)
B [auth I]	SCOP2B Superfamily	RuBisCO, small subunit	8094981	3001622	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)
P [auth L]	V-set	e5n9zL1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
N [auth K]	V-set	e5n9zK1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
L [auth J]	V-set	e5n9zJ1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
J [auth P]	V-set	e5n9zP1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
H [auth M]	V-set	e5n9zM1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
F [auth N]	V-set	e5n9zN1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
D [auth O]	V-set	e5n9zO1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
B [auth I]	Pkinase	e5n9zI1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Pkinase	ECOD (v294.1)
O [auth G]	V-set	e5n9zG1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
M [auth E]	V-set	e5n9zE1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
K [auth C]	V-set	e5n9zC1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
I [auth B]	V-set	e5n9zB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
G [auth D]	V-set	e5n9zD1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
E [auth F]	V-set	e5n9zF1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
C [auth H]	V-set	e5n9zH1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
A	Pkinase	e5n9zA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Pkinase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
P [auth L]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
N [auth K]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
L [auth J]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
J [auth P]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
H [auth M]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
F [auth N]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
D [auth O]	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 I]	3.30.190.10	Alpha Beta	2-Layer Sandwich	Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase	Ribulose bisphosphate carboxylase, small subunit	CATH (4.3.0)
O [auth G]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
O [auth G]	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
M [auth E]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
M [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)
K [auth C]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
K [auth C]	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
I [auth B]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
I [auth B]	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
G [auth D]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
G [auth D]	3.20.20.110	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain	CATH (4.3.0)
E [auth F]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
E [auth F]	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 H]	3.30.70.150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RuBisCO large subunit, N-terminal domain	CATH (4.3.0)
C [auth H]	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
B [auth I], D [auth O], F [auth N], H [auth M], J [auth P], B [auth I], D [auth O], F [auth N], H [auth M], J [auth P], L [auth J], N [auth K], P [auth L]	Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit	ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process cellular 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 H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	Ribulose bisphosphate carboxylase large chain	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding monooxygenase activity oxidoreductase activity catalytic activity ribulose-bisphosphate carboxylase activity carboxy-lyase activity lyase activity carbon-carbon lyase activity	carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction primary metabolic process metabolic process cellular process carbon fixation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth I], D [auth O], F [auth N], H [auth M], J [auth P], B [auth I], D [auth O], F [auth N], H [auth M], J [auth P], L [auth J], N [auth K], P [auth L]	IPR036385	Ribulose bisphosphate carboxylase, small subunit superfamily	Homologous Superfamily
B [auth I], D [auth O], F [auth N], H [auth M], J [auth P], B [auth I], D [auth O], F [auth N], H [auth M], J [auth P], L [auth J], N [auth K], P [auth L]	IPR024681	Ribulose bisphosphate carboxylase, small subunit	Family
B [auth I], D [auth O], F [auth N], H [auth M], J [auth P], B [auth I], D [auth O], F [auth N], H [auth M], J [auth P], L [auth J], N [auth K], P [auth L]	IPR000894	Ribulose bisphosphate carboxylase small subunit, domain	Domain
A, C [auth H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	IPR020888	Ribulose bisphosphate carboxylase large subunit, type I	Family
A, C [auth H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	IPR036376	Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily	Homologous Superfamily
A, C [auth H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	IPR020878	Ribulose bisphosphate carboxylase, large chain, active site	Active Site
A, C [auth H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	IPR000685	Ribulose bisphosphate carboxylase, large subunit, C-terminal	Domain
A, C [auth H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	IPR033966	RuBisCO	Family
A, C [auth H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	IPR036422	RuBisCO large subunit, N-terminal domain superfamily	Homologous Superfamily
A, C [auth H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	IPR017443	Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C [auth H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	8RE	Parent Component: LYS
A, C [auth H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210
A, C [auth H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	HLU	Parent Component: LEU RESID: AA0205
A, C [auth H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	HYP	Parent Component: PRO RESID: AA0205 , AA0030 PSI-MOD : L-cysteine sulfenic acid MOD:00210 , 4-hydroxy-L-proline MOD:00039
A, C [auth H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	KCX	Parent Component: LYS RESID: AA0205 , AA0030
A, C [auth H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	LYO	Parent Component: LYS RESID: AA0205 , AA0030
A, C [auth H], E [auth F], G [auth D], I [auth B], A, C [auth H], E [auth F], G [auth D], I [auth B], K [auth C], M [auth E], O [auth G]	M3L	Parent Component: LYS RESID: AA0205 , AA0030 , AA0074 PSI-MOD : L-cysteine sulfenic acid MOD:00210 , 4-hydroxy-L-proline MOD:00039 , N6,N6,N6-trimethyl-L-lysine MOD:00083