1UP6 | pdb_00001up6

Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.55 Angstrom resolution in the tetragonal form with manganese, 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)
H	d1up6h1	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	d1up6h2	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	d1up6g1	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	d1up6g2	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	d1up6f1	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	d1up6f2	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	d1up6e1	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	d1up6e2	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	d1up6d1	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	d1up6d2	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	d1up6c1	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	d1up6c2	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	d1up6b1	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	d1up6b2	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)
A	d1up6a1	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	d1up6a2	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)
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)
F	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)
D	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)
B	SCOP2B Superfamily	LDH/MDH/AglA-like	8057350	3000039	SCOP2B (2022-06-29)
A	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)
H	Biotin_carb_C	e1up6H1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Biotin_carb_C	ECOD (v294.1)
H	FAD_binding_3	e1up6H2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
G	Biotin_carb_C	e1up6G1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Biotin_carb_C	ECOD (v294.1)
G	FAD_binding_3	e1up6G2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
F	Biotin_carb_C	e1up6F1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Biotin_carb_C	ECOD (v294.1)
F	FAD_binding_3	e1up6F2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
E	Biotin_carb_C	e1up6E1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Biotin_carb_C	ECOD (v294.1)
E	FAD_binding_3	e1up6E2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
D	Biotin_carb_C	e1up6D1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Biotin_carb_C	ECOD (v294.1)
D	FAD_binding_3	e1up6D2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
C	Biotin_carb_C	e1up6C1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Biotin_carb_C	ECOD (v294.1)
C	FAD_binding_3	e1up6C2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
B	Biotin_carb_C	e1up6B1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Biotin_carb_C	ECOD (v294.1)
B	FAD_binding_3	e1up6B2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)
A	Biotin_carb_C	e1up6A1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Biotin_carb_C	ECOD (v294.1)
A	FAD_binding_3	e1up6A2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: FAD_binding_3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)
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)
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)
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)

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.