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)
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)
C	SCOP2B Superfamily	SDR-like	8101615	3000038	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SDR-like	8101615	3000038	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SDR-like	8101615	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)
D	ACS_CODH_B_C	e7kf3D1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: ACS_CODH_B_C	ECOD (develop294)
C	ACS_CODH_B_C	e7kf3C1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: ACS_CODH_B_C	ECOD (develop294)
B	ACS_CODH_B_C	e7kf3B1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: ACS_CODH_B_C	ECOD (develop294)
A	ACS_CODH_B_C	e7kf3A1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: ACS_CODH_B_C	ECOD (develop294)

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.