2BFG | pdb_00002bfg

crystal structure of beta-xylosidase (fam GH39) in complex with dinitrophenyl-beta-xyloside and covalently bound xyloside

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d2bfgh1	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Composite domain of glycosyl hydrolase families 5, 30, 39 and 51	Beta-D-xylosidase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
H	d2bfgh2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	Beta-D-xylosidase, catalytic domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
G	d2bfgg1	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Composite domain of glycosyl hydrolase families 5, 30, 39 and 51	Beta-D-xylosidase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
G	d2bfgg2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	Beta-D-xylosidase, catalytic domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
F	d2bfgf1	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Composite domain of glycosyl hydrolase families 5, 30, 39 and 51	Beta-D-xylosidase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
F	d2bfgf2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	Beta-D-xylosidase, catalytic domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
E	d2bfge1	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Composite domain of glycosyl hydrolase families 5, 30, 39 and 51	Beta-D-xylosidase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
E	d2bfge2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	Beta-D-xylosidase, catalytic domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
D	d2bfgd1	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Composite domain of glycosyl hydrolase families 5, 30, 39 and 51	Beta-D-xylosidase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
D	d2bfgd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	Beta-D-xylosidase, catalytic domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
C	d2bfgc1	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Composite domain of glycosyl hydrolase families 5, 30, 39 and 51	Beta-D-xylosidase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
C	d2bfgc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	Beta-D-xylosidase, catalytic domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d2bfgb1	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Composite domain of glycosyl hydrolase families 5, 30, 39 and 51	Beta-D-xylosidase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d2bfgb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	Beta-D-xylosidase, catalytic domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
A	d2bfga1	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	Composite domain of glycosyl hydrolase families 5, 30, 39 and 51	Beta-D-xylosidase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
A	d2bfga2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	beta-glycanases	Beta-D-xylosidase, catalytic domain	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	(Trans)glycosidases	8032984	3000313	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	(Trans)glycosidases	8032984	3000313	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	(Trans)glycosidases	8032984	3000313	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	(Trans)glycosidases	8032984	3000313	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	(Trans)glycosidases	8032984	3000313	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	(Trans)glycosidases	8032984	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8032984	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8032984	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8032981	3001528	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	e2bfgH1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Ldl_recept_b	F:	ECOD (20:10:01)
H	e2bfgH2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Epimerase	F:	ECOD (20:10:01)
G	e2bfgG1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Ldl_recept_b	F:	ECOD (20:10:01)
G	e2bfgG2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Epimerase	F:	ECOD (20:10:01)
F	e2bfgF1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Ldl_recept_b	F:	ECOD (20:10:01)
F	e2bfgF2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Epimerase	F:	ECOD (20:10:01)
E	e2bfgE1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Ldl_recept_b	F:	ECOD (20:10:01)
E	e2bfgE2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Epimerase	F:	ECOD (20:10:01)
D	e2bfgD1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Ldl_recept_b	F:	ECOD (20:10:01)
D	e2bfgD2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Epimerase	F:	ECOD (20:10:01)
C	e2bfgC1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Ldl_recept_b	F:	ECOD (20:10:01)
C	e2bfgC2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Epimerase	F:	ECOD (20:10:01)
B	e2bfgB1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Ldl_recept_b	F:	ECOD (20:10:01)
B	e2bfgB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Epimerase	F:	ECOD (20:10:01)
A	e2bfgA1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Ldl_recept_b	F:	ECOD (20:10:01)
A	e2bfgA2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Epimerase	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.60.40.1500	Mainly Beta	Sandwich	Immunoglobulin-like	Glycosyl hydrolase domain	CATH (4.3.0)
H	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
G	2.60.40.1500	Mainly Beta	Sandwich	Immunoglobulin-like	Glycosyl hydrolase domain	CATH (4.3.0)
G	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
F	2.60.40.1500	Mainly Beta	Sandwich	Immunoglobulin-like	Glycosyl hydrolase domain	CATH (4.3.0)
F	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
E	2.60.40.1500	Mainly Beta	Sandwich	Immunoglobulin-like	Glycosyl hydrolase domain	CATH (4.3.0)
E	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
D	2.60.40.1500	Mainly Beta	Sandwich	Immunoglobulin-like	Glycosyl hydrolase domain	CATH (4.3.0)
D	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
C	2.60.40.1500	Mainly Beta	Sandwich	Immunoglobulin-like	Glycosyl hydrolase domain	CATH (4.3.0)
C	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
B	2.60.40.1500	Mainly Beta	Sandwich	Immunoglobulin-like	Glycosyl hydrolase domain	CATH (4.3.0)
B	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	2.60.40.1500	Mainly Beta	Sandwich	Immunoglobulin-like	Glycosyl hydrolase domain	CATH (4.3.0)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)

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	BETA-XYLOSIDASE	xylanase activity hydrolase activity, acting on glycosyl bonds xylan 1,4-beta-xylosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity	carbohydrate metabolic process xylan catabolic process catabolic process carbohydrate catabolic process hemicellulose catabolic process primary metabolic process macromolecule catabolic process xylan metabolic process polysaccharide metabolic process polysaccharide catabolic process metabolic process cellular process macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR049166	Glycosyl hydrolases family 39, N-terminal catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000514	Glycoside hydrolase, family 39	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR051923	Glycosyl Hydrolase Family 39	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR049165	Glycosyl hydrolases family 39, active site	Active Site