6W2L | pdb_00006w2l

Crystal structure of human dehydrodolichyl diphosphate synthase (NgBR/DHDDS) in complex with Mg and IPP

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	FAD_binding_3, Pyr_redox_3	e6w2lB1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: FAD_binding_3, Pyr_redox_3	ECOD (v294.1)
A	Cas9_a	e6w2lA01	A: a/b three-layered sandwiches	X: Rossmann-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F: Cas9_a	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01255	Putative undecaprenyl diphosphate synthase (Prenyltransf)	Putative undecaprenyl diphosphate synthase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Dehydrodolichyl diphosphate synthase complex subunit NUS1	prenyl diphosphate synthase activity prenyltransferase activity ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity cation binding ion binding binding metal ion binding small molecule binding	carbohydrate derivative biosynthetic process dolichol-linked oligosaccharide biosynthetic process lipid biosynthetic process glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process protein N-linked glycosylation macromolecule biosynthetic process phospholipid biosynthetic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process carbohydrate derivative biosynthetic process dolichol-linked oligosaccharide biosynthetic process lipid biosynthetic process glycoprotein biosynthetic process carbohydrate derivative metabolic process primary metabolic process glycoprotein metabolic process protein N-linked glycosylation macromolecule biosynthetic process phospholipid biosynthetic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process phosphorus metabolic process dolichyl diphosphate biosynthetic process lipid metabolic process developmental process cellular developmental process cell differentiation multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis regulation of cellular process positive regulation of cell population proliferation endothelial cell proliferation positive regulation of biological process positive regulation of endothelial cell proliferation epithelial cell proliferation positive regulation of cellular process positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis regulation of biological process cell population proliferation blood vessel endothelial cell proliferation involved in sprouting angiogenesis positive regulation of epithelial cell proliferation biological regulation sprouting angiogenesis regulation of endothelial cell proliferation regulation of cell population proliferation regulation of epithelial cell proliferation regulation of localization cellular localization transport regulation of intracellular sterol transport intracellular cholesterol transport regulation of lipid transport organic hydroxy compound transport intracellular sterol transport localization regulation of intracellular cholesterol transport establishment of localization in cell sterol transport regulation of cholesterol transport regulation of intracellular transport regulation of sterol transport regulation of transport intracellular lipid transport regulation of intracellular lipid transport lipid localization lipid transport intracellular transport establishment of localization regulation of lipid localization regulation of cellular localization macromolecule localization cholesterol transport cellular response to stimulus cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus cell surface receptor protein tyrosine kinase signaling pathway cell communication vascular endothelial growth factor signaling pathway cellular response to endogenous stimulus cellular response to vascular endothelial growth factor stimulus signal transduction response to growth factor enzyme-linked receptor protein signaling pathway sterol homeostasis chemical homeostasis homeostatic process cholesterol homeostasis lipid homeostasis dolichyl monophosphate biosynthetic process positive regulation of locomotion regulation of cell motility cell migration involved in sprouting angiogenesis regulation of blood vessel endothelial cell migration endothelial cell migration positive regulation of cell migration positive regulation of cell motility regulation of cell migration blood vessel endothelial cell migration regulation of endothelial cell migration cell migration positive regulation of cell migration involved in sprouting angiogenesis cell motility locomotion regulation of cell migration involved in sprouting angiogenesis positive regulation of blood vessel endothelial cell migration regulation of locomotion positive regulation of endothelial cell migration	protein-containing complex catalytic complex polyprenyl diphosphate synthase complex transferase complex dehydrodolichyl diphosphate synthase complex membrane-bounded organelle intracellular anatomical structure organelle subcompartment membrane intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure protein-containing complex catalytic complex polyprenyl diphosphate synthase complex transferase complex dehydrodolichyl diphosphate synthase complex membrane-bounded organelle intracellular anatomical structure organelle subcompartment membrane intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum membrane
A	Dehydrodolichyl diphosphate synthase complex subunit DHDDS	prenyl diphosphate synthase activity prenyltransferase activity ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity cation binding ion binding binding metal ion binding small molecule binding	polyprenol metabolic process polyprenol biosynthetic process small molecule biosynthetic process isoprenoid biosynthetic process lipid biosynthetic process alcohol metabolic process primary metabolic process biosynthetic process alcohol biosynthetic process small molecule metabolic process metabolic process cellular process isoprenoid metabolic process lipid metabolic process polyprenol metabolic process polyprenol biosynthetic process small molecule biosynthetic process isoprenoid biosynthetic process lipid biosynthetic process alcohol metabolic process primary metabolic process biosynthetic process alcohol biosynthetic process small molecule metabolic process metabolic process cellular process isoprenoid metabolic process lipid metabolic process carbohydrate derivative biosynthetic process dolichol-linked oligosaccharide biosynthetic process glycoprotein biosynthetic process carbohydrate derivative metabolic process glycoprotein metabolic process protein N-linked glycosylation macromolecule biosynthetic process phospholipid biosynthetic process phospholipid metabolic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process protein metabolic process macromolecule metabolic process phosphorus metabolic process dolichyl diphosphate biosynthetic process dolichyl monophosphate biosynthetic process	protein-containing complex catalytic complex polyprenyl diphosphate synthase complex transferase complex dehydrodolichyl diphosphate synthase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system protein-containing complex catalytic complex polyprenyl diphosphate synthase complex transferase complex dehydrodolichyl diphosphate synthase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system organelle subcompartment membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR001441	Decaprenyl diphosphate synthase-like	Family
B	IPR038887	Dehydrodolichyl diphosphate synthase complex subunit Nus1	Family
B	IPR036424	Decaprenyl diphosphate synthase-like superfamily	Homologous Superfamily
A	IPR018520	Di-trans-poly-cis-decaprenylcistransferase-like, conserved site	Conserved Site
A	IPR036424	Decaprenyl diphosphate synthase-like superfamily	Homologous Superfamily
A	IPR001441	Decaprenyl diphosphate synthase-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q96E22	congenital disorder of glycosylation congenital disorder of glycosylation, type IAA melanoma breast cancer Crohn disease inborn errors of metabolism ovarian cancer cutaneous melanoma intellectual disability, autosomal dominant 55, with seizures pancreatic ductal adenocarcinoma endometriosis type 2 diabetes mellitus
A	Pharos: Q86SQ9	retinitis pigmentosa 59 retinitis pigmentosa cone-rod dystrophy ductal breast carcinoma in situ osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia congenital disorder of glycosylation epilepsy pancreatic intraductal papillary-mucinous carcinoma retinal degeneration developmental delay and seizures with or without movement abnormalities invasive ductal breast carcinoma pancreatic intraductal papillary-mucinous neoplasm

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Monotopic/peripheral	Alpha/Beta monotopic/peripheral	Putative undecaprenyl diphosphate synthase	Putative undecaprenyl diphosphate synthase

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.

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