1RPN

Crystal Structure of GDP-D-mannose 4,6-dehydratase in complexes with GDP and NADPH

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	d1rpna_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Tyrosine-dependent oxidoreductases	GDP-mannose 4,6-dehydratase	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
B	d1rpnb_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Tyrosine-dependent oxidoreductases	GDP-mannose 4,6-dehydratase	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
C	d1rpnc_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Tyrosine-dependent oxidoreductases	GDP-mannose 4,6-dehydratase	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
D	d1rpnd_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Tyrosine-dependent oxidoreductases	GDP-mannose 4,6-dehydratase	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	UDP-glucose 4-epimerase GalE-lke	8058504	4000088	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SDR-like	8058505	3000038	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	SDR-like	8058505	3000038	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SDR-like	8058505	3000038	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SDR-like	8058505	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	GDP_Man_Dehyd	e1rpnA1	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	e1rpnB1	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	e1rpnC1	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	e1rpnD1	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)

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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF16363	GDP-mannose 4,6 dehydratase (GDP_Man_Dehyd)	GDP-mannose 4,6 dehydratase	-	Domain

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 organic cyclic compound binding anion binding adenyl nucleotide binding heterocyclic compound binding NADP binding small molecule binding GDP-mannose 4,6-dehydratase activity hydro-lyase activity NADP+ binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound 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	lipopolysaccharide biosynthetic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process cellular biosynthetic process carbohydrate biosynthetic process cellular metabolic process liposaccharide metabolic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process macromolecule biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process organic substance metabolic process lipopolysaccharide biosynthetic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process cellular biosynthetic process carbohydrate biosynthetic process cellular metabolic process liposaccharide metabolic process lipid biosynthetic process carbohydrate derivative metabolic process primary metabolic process macromolecule biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process organic substance metabolic process biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process lipid metabolic process O antigen biosynthetic process O antigen metabolic process nucleotide-sugar metabolic process cellular nitrogen compound metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process heterocycle metabolic process nucleobase-containing small molecule metabolic process nitrogen compound metabolic process small molecule metabolic process GDP-mannose metabolic process cellular aromatic compound metabolic process nucleotide-sugar biosynthetic process phosphorus metabolic process 'de novo' GDP-L-fucose biosynthetic process GDP-L-fucose metabolic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process aromatic compound biosynthetic process organic cyclic compound biosynthetic process GDP-L-fucose biosynthetic process GDP-D-rhamnose biosynthetic process GDP-D-rhamnose 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 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.