8BK7

Cryo-EM structure of beta-galactosidase at 3.3 A resolution plunged 5 ms after mixing with apoferritin

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Galactose mutarotase-like	8037659	3000035	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055462	3002047	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8037663	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055209	3002047	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	galactose-binding domain-like	8037655	3000087	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8037663	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055209	3002047	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Galactose mutarotase-like	8037659	3000035	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	galactose-binding domain-like	8037655	3000087	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055462	3002047	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Galactose mutarotase-like	8037659	3000035	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055462	3002047	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	galactose-binding domain-like	8037655	3000087	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	(Trans)glycosidases	8037663	3000313	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055209	3002047	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055209	3002047	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Galactose mutarotase-like	8037659	3000035	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	galactose-binding domain-like	8037655	3000087	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	(Trans)glycosidases	8037663	3000313	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055462	3002047	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)
A	PF02837	e8bk7A3	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF02837	ECOD (1.6)
A	PF00703	e8bk7A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00703	ECOD (1.6)
A	PF16353	e8bk7A4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF16353	ECOD (1.6)
A	PF02929	e8bk7A2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: PF02929	ECOD (1.6)
A	PF02836	e8bk7A5	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF02836	ECOD (1.6)
B	PF02837	e8bk7B5	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF02837	ECOD (1.6)
B	PF00703	e8bk7B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00703	ECOD (1.6)
B	PF16353	e8bk7B3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF16353	ECOD (1.6)
B	PF02929	e8bk7B1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: PF02929	ECOD (1.6)
B	PF02836	e8bk7B4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF02836	ECOD (1.6)
C	PF02837	e8bk7C3	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF02837	ECOD (1.6)
C	PF00703	e8bk7C5	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00703	ECOD (1.6)
C	PF16353	e8bk7C2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF16353	ECOD (1.6)
C	PF02929	e8bk7C4	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: PF02929	ECOD (1.6)
C	PF02836	e8bk7C1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF02836	ECOD (1.6)
D	PF02837	e8bk7D1	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF02837	ECOD (1.6)
D	PF00703	e8bk7D5	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00703	ECOD (1.6)
D	PF16353	e8bk7D3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF16353	ECOD (1.6)
D	PF02929	e8bk7D4	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: supersandwich (From Topology)	T: supersandwich	F: PF02929	ECOD (1.6)
D	PF02836	e8bk7D2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF02836	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02836	Glycosyl hydrolases family 2, TIM barrel domain (Glyco_hydro_2_C)	Glycosyl hydrolases family 2, TIM barrel domain	This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities.	Domain
A, B, C, D	PF00703	Glycosyl hydrolases family 2 (Glyco_hydro_2)	Glycosyl hydrolases family 2	This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities.	Domain
A, B, C, D	PF02837	Glycosyl hydrolases family 2, sugar binding domain (Glyco_hydro_2_N)	Glycosyl hydrolases family 2, sugar binding domain	This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities and has a jelly-roll fold. The domain binds the sugar moiety during the sugar-hydrolysis reaction.	Domain
A, B, C, D	PF16353	Beta-galactosidase, domain 4 (LacZ_4)	Beta-galactosidase, domain 4	This entry represents domain 4 found in beta-galactosidase [1] and it is organised in a jelly-roll type barrel (Rutkiewicz-Krotewicz M. et al. Crystals 2018, 8(1), 13, https://doi.org/10.3390/cryst8010013).	Domain
A, B, C, D	PF02929	Beta galactosidase small chain (Bgal_small_N)	Beta galactosidase small chain	This domain comprises the small chain of dimeric beta-galactosidases EC:3.2.1.23. This domain is also found in single chain beta-galactosidase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Beta-galactosidase	binding carbohydrate binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding hydrolase activity, acting on glycosyl bonds beta-galactosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity galactosidase activity alkali metal ion binding binding carbohydrate binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding hydrolase activity, acting on glycosyl bonds beta-galactosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity galactosidase activity alkali metal ion binding identical protein binding protein binding	carbohydrate metabolic process catabolic process oligosaccharide catabolic process oligosaccharide metabolic process lactose catabolic process carbohydrate catabolic process primary metabolic process disaccharide metabolic process lactose metabolic process metabolic process disaccharide catabolic process	protein-containing complex catalytic complex beta-galactosidase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR032312	Beta-galactosidase, domain 4	Domain
A, B, C, D	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B, C, D	IPR006101	Glycoside hydrolase, family 2	Family
A, B, C, D	IPR004199	Beta galactosidase small chain/ domain 5	Domain
A, B, C, D	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR006102	Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich	Domain
A, B, C, D	IPR036156	Beta-Galactosidase/glucuronidase domain superfamily	Homologous Superfamily
A, B, C, D	IPR006104	Glycosyl hydrolases family 2, sugar binding domain	Domain
A, B, C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR006103	Glycoside hydrolase family 2, catalytic domain	Domain
A, B, C, D	IPR023232	Glycoside hydrolase, family 2, active site	Active Site
A, B, C, D	IPR023230	Glycoside hydrolase, family 2, conserved site	Conserved Site
A, B, C, D	IPR023933	Glycoside hydrolase, family 2, beta-galactosidase	Family
A, B, C, D	IPR014718	Glycoside hydrolase-type carbohydrate-binding	Homologous Superfamily
A, B, C, D	IPR050347	Bacterial Beta-galactosidase	Family
A, B, C, D	IPR011013	Galactose mutarotase-like domain superfamily	Homologous Superfamily