3SC6

2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP

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	d3sc6a_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	anthrax, anthrax bacterium (Bacillus anthracis str. Ames ) [TaxId: 198094 ],	SCOPe (2.08)
D	d3sc6d1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	anthrax, anthrax bacterium (Bacillus anthracis str. Ames ) [TaxId: 198094 ],	SCOPe (2.08)
D	d3sc6d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	anthrax, anthrax bacterium (Bacillus anthracis str. Ames ) [TaxId: 198094 ],	SCOPe (2.08)
E	d3sc6e_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	anthrax, anthrax bacterium (Bacillus anthracis str. Ames ) [TaxId: 198094 ],	SCOPe (2.08)
B	d3sc6b1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	anthrax, anthrax bacterium (Bacillus anthracis str. Ames ) [TaxId: 198094 ],	SCOPe (2.08)
B	d3sc6b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	anthrax, anthrax bacterium (Bacillus anthracis str. Ames ) [TaxId: 198094 ],	SCOPe (2.08)
C	d3sc6c_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	anthrax, anthrax bacterium (Bacillus anthracis str. Ames ) [TaxId: 198094 ],	SCOPe (2.08)
F	d3sc6f_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	anthrax, anthrax bacterium (Bacillus anthracis str. Ames ) [TaxId: 198094 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SDR-like	8079280	3000038	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SDR-like	8079280	3000038	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	SDR-like	8079280	3000038	SCOP2B (2022-06-29)
B	SCOP2 Family	UDP-glucose 4-epimerase GalE-lke	8079279	4000088	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	SDR-like	8079280	3000038	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	SDR-like	8079280	3000038	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	SDR-like	8079280	3000038	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	RmlD_sub_bind	e3sc6A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: RmlD_sub_bind	ECOD (1.6)
D	RmlD_sub_bind	e3sc6D1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: RmlD_sub_bind	ECOD (1.6)
E	RmlD_sub_bind	e3sc6E1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: RmlD_sub_bind	ECOD (1.6)
B	RmlD_sub_bind	e3sc6B1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: RmlD_sub_bind	ECOD (1.6)
C	RmlD_sub_bind	e3sc6C1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: RmlD_sub_bind	ECOD (1.6)
F	RmlD_sub_bind	e3sc6F1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: RmlD_sub_bind	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	3.90.25.10	Alpha Beta	Alpha-Beta Complex	UDP-galactose 4-epimerase	domain 1	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	3.90.25.10	Alpha Beta	Alpha-Beta Complex	UDP-galactose 4-epimerase	domain 1	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	3.90.25.10	Alpha Beta	Alpha-Beta Complex	UDP-galactose 4-epimerase	domain 1	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	3.90.25.10	Alpha Beta	Alpha-Beta Complex	UDP-galactose 4-epimerase	domain 1	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	3.90.25.10	Alpha Beta	Alpha-Beta Complex	UDP-galactose 4-epimerase	domain 1	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	3.90.25.10	Alpha Beta	Alpha-Beta Complex	UDP-galactose 4-epimerase	domain 1	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	PF04321	RmlD substrate binding domain (RmlD_sub_bind)	RmlD substrate binding domain	L-rhamnose is a saccharide required for the virulence of some bacteria. Its precursor, dTDP-L-rhamnose, is synthesised by four different enzymes the final one of which is RmlD. The RmlD substrate binding domain is responsi ...	L-rhamnose is a saccharide required for the virulence of some bacteria. Its precursor, dTDP-L-rhamnose, is synthesised by four different enzymes the final one of which is RmlD. The RmlD substrate binding domain is responsible for binding a sugar nucleotide [1,2].	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	dTDP-4-dehydrorhamnose reductase	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 dTDP-4-dehydrorhamnose reductase activity binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding	carbohydrate derivative biosynthetic process nucleotide-sugar metabolic process carbohydrate derivative metabolic process primary metabolic process dTDP-rhamnose biosynthetic process nucleobase-containing compound biosynthetic process dTDP-rhamnose metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process nucleobase-containing small molecule metabolic process organic cyclic compound biosynthetic process organic substance biosynthetic process carbohydrate derivative biosynthetic process nucleotide-sugar metabolic process carbohydrate derivative metabolic process primary metabolic process dTDP-rhamnose biosynthetic process nucleobase-containing compound biosynthetic process dTDP-rhamnose metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process nucleobase-containing small molecule metabolic process organic cyclic compound biosynthetic process organic substance biosynthetic process small molecule metabolic process metabolic process nucleotide-sugar biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR029903	RmlD-like substrate binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR005913	dTDP-4-dehydrorhamnose reductase family	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.