1UP4

Structure of the 6-phospho-beta glucosidase from Thermotoga maritima at 2.85 Angstrom resolution in the monoclinic form

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1up4a1	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	d1up4a2	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	d1up4b1	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	d1up4b2	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	d1up4c1	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	d1up4c2	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	d1up4d1	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	d1up4d2	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	d1up4e1	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	d1up4e2	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	d1up4f1	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	d1up4f2	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	d1up4g1	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	d1up4g2	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	d1up4h1	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	d1up4h2	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	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)
C	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)
E	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)
G	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)

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	e1up4A1	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Glyco_hydro_4C	ECOD (1.6)
A	Glyco_hydro_4	e1up4A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Glyco_hydro_4	ECOD (1.6)
B	Glyco_hydro_4C	e1up4B1	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Glyco_hydro_4C	ECOD (1.6)
B	Glyco_hydro_4	e1up4B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Glyco_hydro_4	ECOD (1.6)
C	Glyco_hydro_4C	e1up4C1	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Glyco_hydro_4C	ECOD (1.6)
C	Glyco_hydro_4	e1up4C2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Glyco_hydro_4	ECOD (1.6)
D	Glyco_hydro_4C	e1up4D1	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Glyco_hydro_4C	ECOD (1.6)
D	Glyco_hydro_4	e1up4D2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Glyco_hydro_4	ECOD (1.6)
E	Glyco_hydro_4C	e1up4E1	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Glyco_hydro_4C	ECOD (1.6)
E	Glyco_hydro_4	e1up4E2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Glyco_hydro_4	ECOD (1.6)
F	Glyco_hydro_4C	e1up4F1	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Glyco_hydro_4C	ECOD (1.6)
F	Glyco_hydro_4	e1up4F2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Glyco_hydro_4	ECOD (1.6)
G	Glyco_hydro_4C	e1up4G1	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Glyco_hydro_4C	ECOD (1.6)
G	Glyco_hydro_4	e1up4G2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Glyco_hydro_4	ECOD (1.6)
H	Glyco_hydro_4C	e1up4H1	A: a+b complex topology	X: LDH C-terminal domain-like (From Topology)	H: LDH C-terminal domain-like (From Topology)	T: LDH C-terminal domain-like	F: Glyco_hydro_4C	ECOD (1.6)
H	Glyco_hydro_4	e1up4H2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Glyco_hydro_4	ECOD (1.6)

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)
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)
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)
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)
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)
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)
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)

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	hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity methyl beta-D-glucoside 6-phosphate glucohydrolase activity catalytic 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 cation binding ion binding binding metal ion binding small molecule binding glucosidase activity hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity methyl beta-D-glucoside 6-phosphate glucohydrolase activity catalytic 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 cation binding ion binding binding metal ion binding small molecule binding glucosidase activity 6-phospho-beta-glucosidase activity beta-glucosidase activity	carbohydrate metabolic process organic substance metabolic process primary metabolic process 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	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 National Science Foundation (DBI-1832184), 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 R01GM133198.