1UP7 | pdb_00001up7

Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.4 Angstrom resolution in the tetragonal form with NAD and glucose-6-phosphate

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	d1up7a1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
A	d1up7a2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	AglA-like glucosidase	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
B	d1up7b1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
B	d1up7b2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	AglA-like glucosidase	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
D	d1up7d1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
D	d1up7d2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	AglA-like glucosidase	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
F	d1up7f1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
F	d1up7f2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	AglA-like glucosidase	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
H	d1up7h1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
H	d1up7h2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	AglA-like glucosidase	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
G	d1up7g1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
G	d1up7g2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	AglA-like glucosidase	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
E	d1up7e1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
E	d1up7e2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	AglA-like glucosidase	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
C	d1up7c1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	LDH N-terminal domain-like	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
C	d1up7c2	Alpha and beta proteins (a+b)	LDH C-terminal domain-like	LDH C-terminal domain-like	AglA-like glucosidase	6-phospho-beta-glucosidase	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	AglA-like	8057349	4000089	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LDH/MDH/AglA-like	8057350	3000039	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	LDH/MDH/AglA-like	8057350	3000039	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	LDH/MDH/AglA-like	8057350	3000039	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	LDH/MDH/AglA-like	8057350	3000039	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	LDH/MDH/AglA-like	8057350	3000039	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	LDH/MDH/AglA-like	8057350	3000039	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	LDH/MDH/AglA-like	8057350	3000039	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	LDH/MDH/AglA-like	8057350	3000039	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	Glyco_hydro_4C	e1up7A1	A: few secondary structure elements	X: LDH C-terminal domain-like	H: LDH C-terminal domain-like	T: LDH C-terminal domain-like	F: Glyco_hydro_4C	ECOD (develop294)
A	FAD_binding_3	e1up7A2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
B	Biotin_carb_C	e1up7B1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Biotin_carb_C	ECOD (develop294)
B	FAD_binding_3	e1up7B2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
D	Biotin_carb_C	e1up7D1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Biotin_carb_C	ECOD (develop294)
D	FAD_binding_3	e1up7D2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
F	Biotin_carb_C	e1up7F1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Biotin_carb_C	ECOD (develop294)
F	FAD_binding_3	e1up7F2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
H	Biotin_carb_C	e1up7H1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Biotin_carb_C	ECOD (develop294)
H	FAD_binding_3	e1up7H2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
G	Biotin_carb_C	e1up7G1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Biotin_carb_C	ECOD (develop294)
G	FAD_binding_3	e1up7G2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
E	Biotin_carb_C	e1up7E1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Biotin_carb_C	ECOD (develop294)
E	FAD_binding_3	e1up7E2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)
C	Biotin_carb_C	e1up7C1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Biotin_carb_C	ECOD (develop294)
C	FAD_binding_3	e1up7C2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
H	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
G	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	3.90.110.10	Alpha Beta	Alpha-Beta Complex	L-2-Hydroxyisocaproate Dehydrogenase	Chain A, domain 2	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	PF02056	Family 4 glycosyl hydrolase (Glyco_hydro_4)	Family 4 glycosyl hydrolase	-	Family
A, B, C, D, E A, B, C, D, E, F, G, H	PF11975	Family 4 glycosyl hydrolase C-terminal domain (Glyco_hydro_4C)	Family 4 glycosyl hydrolase C-terminal domain		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	6-PHOSPHO-BETA-GLUCOSIDASE	oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors catalytic activity hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity cation binding ion binding binding metal ion binding small molecule binding glucosidase activity 6-phospho-beta-glucosidase activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors catalytic activity hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity cation binding ion binding binding metal ion binding small molecule binding glucosidase activity 6-phospho-beta-glucosidase activity beta-glucosidase activity	carbohydrate metabolic process primary metabolic process metabolic process cellular process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR022616	Glycosyl hydrolase, family 4, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR019802	Glycoside hydrolase, family 4, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015955	Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001088	Glycoside hydrolase, family 4	Family

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.