3KHU | pdb_00003khu

Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	SBP_bac_1	e3khuF1	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: SBP_bac_1	ECOD (develop294)
E	UvrB_inter	e3khuE1	A: alpha bundles	X: Anticodon-binding domain of Class II aaRS	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: UvrB_inter	ECOD (develop294)
D	SBP_bac_1	e3khuD1	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: SBP_bac_1	ECOD (develop294)
C	SBP_bac_1	e3khuC1	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: SBP_bac_1	ECOD (develop294)
B	SBP_bac_1	e3khuB1	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: SBP_bac_1	ECOD (develop294)
A	RrnaAD	e3khuA1	A: alpha bundles	X: Alpha-beta plaits	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: RrnaAD	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F	1.20.5.100	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Cytochrome c1, transmembrane anchor, C-terminal	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	1.20.5.100	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Cytochrome c1, transmembrane anchor, C-terminal	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	1.20.5.100	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Cytochrome c1, transmembrane anchor, C-terminal	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	1.20.5.100	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Cytochrome c1, transmembrane anchor, C-terminal	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	1.20.5.100	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Cytochrome c1, transmembrane anchor, C-terminal	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	1.20.5.100	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Cytochrome c1, transmembrane anchor, C-terminal	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF03720	UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain (UDPG_MGDP_dh_C)	UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain	The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [2].	Domain
A, B, C, D, E A, B, C, D, E, F	PF03721	UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain (UDPG_MGDP_dh_N)	UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain	The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [2].	Domain
A, B, C, D, E A, B, C, D, E, F	PF00984	UDP-glucose/GDP-mannose dehydrogenase family, central domain (UDPG_MGDP_dh)	UDP-glucose/GDP-mannose dehydrogenase family, central domain	The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	UDP-glucose 6-dehydrogenase	NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors UDP-glucose 6-dehydrogenase activity catalytic activity identical protein binding NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors UDP-glucose 6-dehydrogenase activity catalytic activity identical protein binding protein binding	oxoacid metabolic process UDP-glucuronate metabolic process carbohydrate derivative metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process UDP-glucuronate biosynthetic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleotide-sugar biosynthetic process nucleoside phosphate metabolic process oxoacid metabolic process UDP-glucuronate metabolic process carbohydrate derivative metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process UDP-glucuronate biosynthetic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleotide-sugar biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process small molecule biosynthetic process nucleotide-sugar metabolic process carboxylic acid metabolic process primary metabolic process nucleobase-containing compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process developmental process multicellular organism development multicellular organismal process anatomical structure morphogenesis gastrulation with mouth forming second embryonic morphogenesis anatomical structure development embryo development gastrulation glycosaminoglycan metabolic process macromolecule biosynthetic process aminoglycan metabolic process aminoglycan biosynthetic process glycosaminoglycan biosynthetic process macromolecule metabolic process cellular component organization cellular component biogenesis protein hexamerization cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis proteoglycan biosynthetic process glycoprotein biosynthetic process chondroitin sulfate proteoglycan metabolic process glycoprotein metabolic process protein O-linked glycosylation via xylose protein O-linked glycosylation protein metabolic process chondroitin sulfate proteoglycan biosynthetic process proteoglycan metabolic process heparan sulfate proteoglycan biosynthetic process heparan sulfate proteoglycan metabolic process cellular developmental process cell development nervous system development generation of neurons neurogenesis neuron differentiation cell differentiation neuron development system development	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 nucleus 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 nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR028356	UDP-glucose 6-dehydrogenase, eukaryotic type	Family
A, B, C, D, E A, B, C, D, E, F	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR017476	UDP-glucose/GDP-mannose dehydrogenase	Family
A, B, C, D, E A, B, C, D, E, F	IPR014026	UDP-glucose/GDP-mannose dehydrogenase, dimerisation	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014027	UDP-glucose/GDP-mannose dehydrogenase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036220	UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001732	UDP-glucose/GDP-mannose dehydrogenase, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: O60701	liver cancer atypical teratoid rhabdoid tumor glioblastoma malignant glioma pancreatic ductal adenocarcinoma primitive neuroectodermal tumor breast cancer herpes zoster liver neoplasm medulloblastoma peripheral arterial disease sinusitis epilepsy interstitial cystitis malignant colon neoplasm liver cancer atypical teratoid rhabdoid tumor glioblastoma malignant glioma pancreatic ductal adenocarcinoma primitive neuroectodermal tumor breast cancer herpes zoster liver neoplasm medulloblastoma peripheral arterial disease sinusitis epilepsy interstitial cystitis malignant colon neoplasm ovarian cancer pilocytic astrocytoma 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.