6GPK | pdb_00006gpk

Crystal structure of human GDP-D-mannose 4,6-dehydratase (E157Q) in complex with GDP-Man

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	d6gpkd_	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	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6gpkc_	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	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6gpkb_	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	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6gpka_	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	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	8058507	3000038	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SDR-like	8058507	3000038	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SDR-like	8058507	3000038	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SDR-like	8058507	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	Anoctamin	e6gpkD1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (develop294)
C	Anoctamin	e6gpkC1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (develop294)
B	Anoctamin	e6gpkB1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (develop294)
A	Anoctamin	e6gpkA1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (develop294)

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	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 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 identical protein binding protein binding	nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process nucleotide-sugar metabolic process carbohydrate derivative metabolic 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 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 cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell communication Notch signaling pathway signal transduction 'de novo' 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	IPR016040	NAD(P)-binding domain	Domain
A, B, C, D	IPR006368	GDP-mannose 4,6-dehydratase	Family
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O60547	ulcerative colitis astrocytic tumor ductal breast carcinoma in situ lung cancer nasopharyngeal carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia spina bifida brachydactyly type E1 heart disease lung carcinoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma tuberculosis ulcerative colitis astrocytic tumor ductal breast carcinoma in situ lung cancer nasopharyngeal carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia spina bifida brachydactyly type E1 heart disease lung carcinoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma tuberculosis Crohn disease lung adenocarcinoma medulloblastoma open-angle glaucoma pancreatic intraductal papillary-mucinous neoplasm psoriasis

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.