3VD9 | pdb_00003vd9

E. coli (lacZ) beta-galactosidase (N460S) in complex with IPTG

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)
A	d3vd9a2	All beta proteins	Immunoglobulin-like beta-sandwich	beta-Galactosidase/glucuronidase domain	beta-Galactosidase/glucuronidase domain	beta-Galactosidase, domains 2 and 4	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d3vd9a1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	beta-Galactosidase/glucuronidase, N-terminal domain	beta-Galactosidase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d3vd9a5	All beta proteins	Supersandwich	Galactose mutarotase-like	beta-Galactosidase, domain 5	beta-Galactosidase, domain 5	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d3vd9a3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	beta-Galactosidase, domain 3	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d3vd9d2	All beta proteins	Immunoglobulin-like beta-sandwich	beta-Galactosidase/glucuronidase domain	beta-Galactosidase/glucuronidase domain	beta-Galactosidase, domains 2 and 4	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d3vd9d1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	beta-Galactosidase/glucuronidase, N-terminal domain	beta-Galactosidase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d3vd9d5	All beta proteins	Supersandwich	Galactose mutarotase-like	beta-Galactosidase, domain 5	beta-Galactosidase, domain 5	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d3vd9d3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	beta-Galactosidase, domain 3	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d3vd9c2	All beta proteins	Immunoglobulin-like beta-sandwich	beta-Galactosidase/glucuronidase domain	beta-Galactosidase/glucuronidase domain	beta-Galactosidase, domains 2 and 4	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d3vd9c1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	beta-Galactosidase/glucuronidase, N-terminal domain	beta-Galactosidase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d3vd9c5	All beta proteins	Supersandwich	Galactose mutarotase-like	beta-Galactosidase, domain 5	beta-Galactosidase, domain 5	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d3vd9c3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	beta-Galactosidase, domain 3	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d3vd9b2	All beta proteins	Immunoglobulin-like beta-sandwich	beta-Galactosidase/glucuronidase domain	beta-Galactosidase/glucuronidase domain	beta-Galactosidase, domains 2 and 4	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d3vd9b1	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	beta-Galactosidase/glucuronidase, N-terminal domain	beta-Galactosidase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d3vd9b5	All beta proteins	Supersandwich	Galactose mutarotase-like	beta-Galactosidase, domain 5	beta-Galactosidase, domain 5	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d3vd9b3	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	beta-Galactosidase, domain 3	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d3vd9b6	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	galactose-binding domain-like	8037655	3000087	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055462	3002047	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Galactose mutarotase-like	8037659	3000035	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055209	3002047	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8037663	3000313	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	galactose-binding domain-like	8037655	3000087	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	beta-Galactosidase/glucuronidase domain-like	8055209	3002047	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	(Trans)glycosidases	8037663	3000313	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Galactose mutarotase-like	8037659	3000035	SCOP2B (2022-06-29)
D	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	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	beta-Galactosidase/glucuronidase domain-like	8055209	3002047	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)
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	(Trans)glycosidases	8037663	3000313	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	e3vd9A11	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T: C1-set	F:	ECOD (20:10:01)
D	e3vd9D11	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T: C1-set	F:	ECOD (20:10:01)
C	e3vd9C11	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T: C1-set	F:	ECOD (20:10:01)
B	e3vd9B11	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T: C1-set	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	2.70.98.10	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
D	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
D	2.70.98.10	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
C	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
C	2.70.98.10	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)
B	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
B	2.70.98.10	Mainly Beta	Distorted Sandwich	Beta-galactosidase	Chain A, domain 5	CATH (4.3.0)

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 cellular 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	IPR006102	Glycoside hydrolase family 2, immunoglobulin-like beta-sandwich	Domain
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	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