5DBU | pdb_00005dbu

Crystal structure of 2-deoxyribose-5-phosphate aldolase (1-220) from Streptococcus suis

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)
M	d5dbum_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Streptococcus suis GZ1 ) [TaxId: 423211 ],	SCOPe (2.08)
L	d5dbul_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Streptococcus suis GZ1 ) [TaxId: 423211 ],	SCOPe (2.08)
K	d5dbuk_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Streptococcus suis GZ1 ) [TaxId: 423211 ],	SCOPe (2.08)
J	d5dbuj_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Streptococcus suis GZ1 ) [TaxId: 423211 ],	SCOPe (2.08)
I	d5dbui_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Streptococcus suis GZ1 ) [TaxId: 423211 ],	SCOPe (2.08)
H	d5dbuh_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Streptococcus suis GZ1 ) [TaxId: 423211 ],	SCOPe (2.08)
G	d5dbug_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Streptococcus suis GZ1 ) [TaxId: 423211 ],	SCOPe (2.08)
F	d5dbuf_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Streptococcus suis GZ1 ) [TaxId: 423211 ],	SCOPe (2.08)
E	d5dbue_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Streptococcus suis GZ1 ) [TaxId: 423211 ],	SCOPe (2.08)
D	d5dbud_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Streptococcus suis GZ1 ) [TaxId: 423211 ],	SCOPe (2.08)
C	d5dbuc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Streptococcus suis GZ1 ) [TaxId: 423211 ],	SCOPe (2.08)
B	d5dbub_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Streptococcus suis GZ1 ) [TaxId: 423211 ],	SCOPe (2.08)
A	d5dbua_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	automated matches	automated matches	(Streptococcus suis GZ1 ) [TaxId: 423211 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
M	SCOP2B Superfamily	Aldolase	8066587	3000445	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Aldolase	8066587	3000445	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Aldolase	8066587	3000445	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Aldolase	8066587	3000445	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Aldolase	8066587	3000445	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Aldolase	8066587	3000445	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Aldolase	8066587	3000445	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Aldolase	8066587	3000445	SCOP2B (2022-06-29)
E	SCOP2 Family	Class I aldolase	8066586	4003216	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Aldolase	8066587	3000445	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Aldolase	8066587	3000445	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Aldolase	8066587	3000445	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aldolase	8066587	3000445	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Aldolase	8066587	3000445	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)
M	DeoC_1	e5dbuM1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)
L	DeoC_1	e5dbuL1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)
K	DeoC_1	e5dbuK1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)
J	DeoC_1	e5dbuJ1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)
I	DeoC_1	e5dbuI1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)
H	DeoC_1	e5dbuH1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)
G	DeoC_1	e5dbuG1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)
F	DeoC_1	e5dbuF1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)
E	DeoC_1	e5dbuE1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)
D	DeoC_1	e5dbuD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)
C	DeoC_1	e5dbuC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)
B	DeoC_1	e5dbuB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)
A	DeoC_1	e5dbuA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DeoC_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
M	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
L	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
K	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
J	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
I	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
H	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
G	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
F	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
E	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	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, K, L, M	PF01791	DeoC/LacD family aldolase (DeoC)	DeoC/LacD family aldolase	This family includes diverse aldolase enzymes. This family includes the enzyme deoxyribose-phosphate aldolase EC:4.1.2.4, which is involved in nucleotide metabolism. The family also includes a group of related bacterial proteins of unknown function, ...	This family includes diverse aldolase enzymes. This family includes the enzyme deoxyribose-phosphate aldolase EC:4.1.2.4, which is involved in nucleotide metabolism. The family also includes a group of related bacterial proteins of unknown function, see examples Swiss:Q57843 and Swiss:P76143. The family also includes tagatose 1,6-diphosphate aldolase (EC:4.1.2.40) is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation [2].	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, K, L, M	Deoxyribose-phosphate aldolase	deoxyribose-phosphate aldolase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity	carbohydrate derivative catabolic process catabolic process carbohydrate derivative metabolic process organophosphate catabolic process deoxyribose phosphate catabolic process organophosphate metabolic process 2-deoxyribose 1-phosphate catabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process carbohydrate metabolic process carbohydrate catabolic process primary metabolic process carbohydrate derivative catabolic process catabolic process carbohydrate derivative metabolic process organophosphate catabolic process deoxyribose phosphate catabolic process organophosphate metabolic process 2-deoxyribose 1-phosphate catabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process carbohydrate metabolic process carbohydrate catabolic process primary metabolic process nucleoside phosphate metabolic process deoxyribonucleotide catabolic process nucleoside phosphate catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process nucleotide catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

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, K, L, M	IPR011343	Deoxyribose-phosphate aldolase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	IPR002915	DeoC/FbaB/LacD aldolase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	IPR028581	Deoxyribose-phosphate aldolase type I	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily

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.