4B8Z | pdb_00004b8z

Crystal structure of human GDP-L-fucose synthase with bound NADP and GDP, rhombohedral crystal form

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4b8zd_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4b8zc_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4b8zb1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4b8zb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4b8za_	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	SDR-like	8079441	3000038	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SDR-like	8079441	3000038	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SDR-like	8079441	3000038	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SDR-like	8079441	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	GDP_Man_Dehyd_1	e4b8zD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GDP_Man_Dehyd_1	ECOD (1.6)
C	GDP_Man_Dehyd_1	e4b8zC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GDP_Man_Dehyd_1	ECOD (1.6)
B	GDP_Man_Dehyd_1	e4b8zB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GDP_Man_Dehyd_1	ECOD (1.6)
A	GDP_Man_Dehyd_1	e4b8zA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: GDP_Man_Dehyd_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)

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-L-FUCOSE SYNTHASE	oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor GDP-4-dehydro-D-rhamnose reductase activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity GDP-mannose 3,5-epimerase activity isomerase activity racemase and epimerase activity racemase and epimerase activity, acting on carbohydrates and derivatives GDP-L-fucose synthase activity electron transfer activity identical protein binding protein binding binding	positive regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process endothelial cell migration biological regulation positive regulation of biological process positive regulation of cell migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration cell migration positive regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process endothelial cell migration biological regulation positive regulation of biological process positive regulation of cell migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration cell migration cellular process cell motility locomotion positive regulation of cellular process nucleoside phosphate metabolic process nucleotide-sugar metabolic process carbohydrate derivative metabolic process primary metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process small molecule metabolic process phosphorus metabolic process GDP-mannose metabolic process cell adhesion cell-cell adhesion leukocyte cell-cell adhesion adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains T cell mediated cytotoxicity lymphocyte mediated immunity T cell mediated immunity response to stimulus immune response leukocyte mediated cytotoxicity adaptive immune response immune effector process immune system process leukocyte mediated immunity cell killing endothelial cell-matrix adhesion regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion positive regulation of cell-matrix adhesion positive regulation of endothelial cell-matrix adhesion cell-matrix adhesion positive regulation of cell-substrate adhesion regulation of cell-matrix adhesion regulation of endothelial cell-matrix adhesion carbohydrate derivative biosynthetic process 'de novo' GDP-L-fucose biosynthetic process GDP-L-fucose metabolic process nucleobase-containing compound biosynthetic process biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process nucleotide-sugar biosynthetic process GDP-L-fucose biosynthetic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR028614	GDP-L-fucose synthase/GDP-L-colitose synthase	Family
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR001509	NAD-dependent epimerase/dehydratase	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q13630	atopic eczema diabetes mellitus lung adenocarcinoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast cancer ductal breast carcinoma in situ lung carcinoma osteosarcoma psoriasis breast carcinoma invasive ductal breast carcinoma malignant pancreatic neoplasm ovarian cancer ulcerative colitis

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.