7KF3 | pdb_00007kf3

Crystal structure of GDP-mannose 4,6-dehydratase from Brucella abortus (strain 2308) in complex with Guanosine-diphosphate-rhamnose

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SDR-like	8101615	3000038	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SDR-like	8101615	3000038	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SDR-like	8101615	3000038	SCOP2B (2022-06-29)
D	SCOP2 Family	UDP-glucose 4-epimerase GalE-lke	8101614	4000088	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	SDR-like	8101615	3000038	SCOP2 (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	GDP_Man_Dehyd	e7kf3A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GDP_Man_Dehyd	ECOD (1.6)
B	GDP_Man_Dehyd	e7kf3B1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GDP_Man_Dehyd	ECOD (1.6)
C	GDP_Man_Dehyd	e7kf3C1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GDP_Man_Dehyd	ECOD (1.6)
D	GDP_Man_Dehyd	e7kf3D1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GDP_Man_Dehyd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01370	NAD dependent epimerase/dehydratase family (Epimerase)	NAD dependent epimerase/dehydratase family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	GDP-mannose 4,6-dehydratase	NADP+ binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding NADP binding small molecule binding GDP-mannose 4,6-dehydratase activity hydro-lyase activity lyase activity NADP+ binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding NADP binding small molecule binding GDP-mannose 4,6-dehydratase activity hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity	nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process nucleotide-sugar metabolic process carbohydrate derivative metabolic process 'de novo' GDP-L-fucose biosynthetic process primary metabolic process GDP-L-fucose metabolic process nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process nucleotide-sugar metabolic process carbohydrate derivative metabolic process 'de novo' GDP-L-fucose biosynthetic process primary metabolic process GDP-L-fucose metabolic process nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process nucleotide-sugar biosynthetic process phosphorus metabolic process GDP-L-fucose biosynthetic process GDP-mannose metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR016040	NAD(P)-binding domain	Domain
A, B, C, D	IPR006368	GDP-mannose 4,6-dehydratase	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.