3EMK | pdb_00003emk

2.5A crystal structure of glucose/ribitol dehydrogenase from brucella melitensis

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	d3emka1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Brucella melitensis ) [TaxId: 29459 ],	SCOPe (2.08)
A	d3emka2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Brucella melitensis ) [TaxId: 29459 ],	SCOPe (2.08)
B	d3emkb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Brucella melitensis ) [TaxId: 29459 ],	SCOPe (2.08)
B	d3emkb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Brucella melitensis ) [TaxId: 29459 ],	SCOPe (2.08)
C	d3emkc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Brucella melitensis ) [TaxId: 29459 ],	SCOPe (2.08)
C	d3emkc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Brucella melitensis ) [TaxId: 29459 ],	SCOPe (2.08)
D	d3emkd1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Brucella melitensis ) [TaxId: 29459 ],	SCOPe (2.08)
D	d3emkd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Brucella melitensis ) [TaxId: 29459 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Short-chain dehydrogenases/reductases, SDR	8063195	4000029	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SDR-like	8063196	3000038	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	SDR-like	8063196	3000038	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SDR-like	8063196	3000038	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SDR-like	8063196	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	FXa_inhibition	e3emkA1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: FXa_inhibition	ECOD (v294.1)
B	FXa_inhibition	e3emkB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: FXa_inhibition	ECOD (v294.1)
C	FXa_inhibition	e3emkC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: FXa_inhibition	ECOD (v294.1)
D	FXa_inhibition	e3emkD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: FXa_inhibition	ECOD (v294.1)

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)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	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)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13561	Enoyl-(Acyl carrier protein) reductase (adh_short_C2)	Enoyl-(Acyl carrier protein) reductase	This domain is found in Enoyl-(Acyl carrier protein) reductases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	GLUCOSE/RIBITOL DEHYDROGENASE	NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) 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	fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process lipid biosynthetic process primary metabolic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process biosynthetic process small molecule metabolic process metabolic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process lipid biosynthetic process primary metabolic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process biosynthetic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR011284	3-oxoacyl-(acyl-carrier-protein) reductase	Family
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR057326	Ketoreductase domain	Domain
A, B, C, D	IPR002347	Short-chain dehydrogenase/reductase SDR	Family
A, B, C, D	IPR050259	Short-chain dehydrogenases/reductases	Family
A, B, C, D	IPR020904	Short-chain dehydrogenase/reductase, conserved site	Conserved Site

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.