Annotations: 9OYA

Full LRRK2 (R1441C mutant) after symmetry expansion

External Resource: Annotation

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Leucine-rich repeat serine/threonine-protein kinase 2	protein-containing complex binding binding beta-catenin destruction complex binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding protein-containing complex binding binding beta-catenin destruction complex binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cytoskeletal protein binding microtubule binding protein binding tubulin binding protein serine/threonine kinase activity JUN kinase kinase kinase activity MAP kinase kinase kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides clathrin binding syntaxin-1 binding SNARE binding syntaxin binding guanyl nucleotide binding GTP binding guanyl ribonucleotide binding cation binding magnesium ion binding metal ion binding GTP-dependent protein kinase activity identical protein binding protein homodimerization activity protein dimerization activity co-receptor binding small GTPase binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity molecular function inhibitor activity peroxidase inhibitor activity enzyme inhibitor activity protein kinase A binding protein serine kinase activity transmembrane transporter binding actin binding signaling receptor complex adaptor activity protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity	cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus regulation of Wnt signaling pathway signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway biological regulation regulation of signal transduction cell communication regulation of response to stimulus cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus regulation of Wnt signaling pathway signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway biological regulation regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication cellular process signal transduction Wnt signaling pathway developmental process multicellular organismal process head development forebrain development olfactory lobe development animal organ development brain development nervous system development tangential migration from the subventricular zone to the olfactory bulb multicellular organism development telencephalon cell migration central nervous system development forebrain cell migration anatomical structure development cell migration telencephalon development cell motility olfactory bulb development animal gross anatomical part developmental process system development catabolic process autophagy metabolic process process utilizing autophagic mechanism intracellular signal transduction regulation of CAMKK-AMPK signaling cascade calcium-mediated signaling regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling CAMKK-AMPK signaling cascade regulation of cellular component organization regulation of developmental process organelle fission mitochondrial fission regulation of organelle organization cellular component organization anatomical structure morphogenesis organelle organization regulation of mitochondrial fission regulation of mitochondrion organization cellular component organization or biogenesis regulation of anatomical structure morphogenesis mitochondrion organization positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of protein metabolic process primary metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process regulation of localization import into cell cellular localization transport synaptic vesicle cycle regulation of synaptic vesicle recycling vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse localization synaptic vesicle recycling regulation of synaptic vesicle endocytosis establishment of localization in cell regulation of endocytosis synaptic vesicle endocytosis regulation of transport establishment of localization endocytosis response to oxidative stress cellular response to chemical stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress regulation of cAMP/PKA signal transduction cAMP/PKA signal transduction cellular response to nutrient levels response to nutrient levels response to starvation cellular response to starvation cellular response to nitrogen compound response to dopamine cellular response to dopamine response to monoamine regulation of dopamine receptor signaling pathway response to catecholamine cellular response to catecholamine stimulus regulation of G protein-coupled receptor signaling pathway G protein-coupled dopamine receptor signaling pathway response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to monoamine stimulus G protein-coupled receptor signaling pathway JNK cascade MAPK cascade protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein modification process regulation of biological quality regulation of membrane potential regulation of ER to Golgi vesicle-mediated transport intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport regulation of vesicle-mediated transport regulation of cellular localization Golgi vesicle transport regulation of intracellular transport regulation of morphogenesis of a branching structure regulation of branching morphogenesis of a nerve morphogenesis of a branching structure branching morphogenesis of a nerve regulation of multicellular organismal process small GTPase-mediated signal transduction Rho protein signal transduction nucleoside phosphate metabolic process ribose phosphate metabolic process purine nucleoside triphosphate metabolic process GTP metabolic process carbohydrate derivative metabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process small molecule metabolic process nucleoside triphosphate metabolic process phosphorus metabolic process purine ribonucleotide metabolic process positive regulation of autophagy regulation of autophagy cell projection organization motile cilium assembly negative regulation of biological process negative regulation of organelle assembly plasma membrane bounded cell projection assembly negative regulation of motile cilium assembly cellular component biogenesis negative regulation of plasma membrane bounded cell projection assembly cellular component assembly cilium assembly negative regulation of cellular process negative regulation of cell projection organization cilium organization organelle assembly plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly regulation of cilium assembly negative regulation of organelle organization regulation of organelle assembly negative regulation of cilium assembly regulation of motile cilium assembly cell projection assembly regulation of plasma membrane bounded cell projection organization neuron projection development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation regulation of synapse structure or activity synapse organization dendritic spine morphogenesis dendritic spine development postsynapse organization dendritic spine organization regulation of postsynapse organization generation of neurons regulation of neuron projection development cellular developmental process plasma membrane bounded cell projection morphogenesis cell development cell morphogenesis neurogenesis dendrite development dendrite morphogenesis cell morphogenesis involved in neuron differentiation regulation of synapse organization cell junction organization neuron development regulation of dendritic spine morphogenesis neuron projection organization endosomal transport cytosolic transport retrograde transport, endosome to Golgi regulation of retrograde transport, endosome to Golgi negative regulation of signaling negative regulation of intracellular signal transduction regulation of cellular response to stress regulation of response to endoplasmic reticulum stress negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway regulation of programmed cell death intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress regulation of intrinsic apoptotic signaling pathway negative regulation of cell communication regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway regulation of response to stress negative regulation of apoptotic signaling pathway intrinsic apoptotic signaling pathway response to endoplasmic reticulum stress negative regulation of response to endoplasmic reticulum stress negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic process apoptotic process programmed cell death regulation of apoptotic signaling pathway regulation of protein modification process regulation of protein ubiquitination positive regulation of post-translational protein modification positive regulation of protein modification process protein ubiquitination regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of protein autoubiquitination protein autoubiquitination positive regulation of protein autoubiquitination cellular response to metal ion response to metal ion cellular response to manganese ion response to manganese ion behavior locomotory behavior exploration behavior locomotory exploration behavior endoplasmic reticulum organization endomembrane system organization regulation of postsynaptic membrane potential system process chemical synaptic transmission, postsynaptic synaptic signaling trans-synaptic signaling nervous system process cell-cell signaling chemical synaptic transmission anterograde trans-synaptic signaling excitatory postsynaptic potential mitochondrion localization organelle localization regulation of protein maturation negative regulation of proteolysis negative regulation of protein maturation protein maturation regulation of proteolysis proteolysis negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of protein processing protein processing regulation of macromolecule biosynthetic process negative regulation of protein processing protein localization to organelle macromolecule localization protein localization to mitochondrion intracellular protein localization positive regulation of programmed cell death macroautophagy autophagosome organization negative regulation of autophagosome assembly negative regulation of catabolic process autophagosome assembly vacuole organization regulation of autophagosome assembly regulation of vacuole organization negative regulation of macroautophagy regulation of macroautophagy negative regulation of autophagy positive regulation of cell communication positive regulation of signal transduction positive regulation of response to stimulus positive regulation of G protein-coupled receptor signaling pathway positive regulation of dopamine receptor signaling pathway positive regulation of signaling positive regulation of Wnt signaling pathway positive regulation of canonical Wnt signaling pathway regulation of tumor necrosis factor production positive regulation of macromolecule biosynthetic process positive regulation of tumor necrosis factor superfamily cytokine production positive regulation of biosynthetic process cytokine production regulation of cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production positive regulation of organelle organization positive regulation of cellular component organization apoptotic mitochondrial changes mitochondrial outer membrane permeabilization involved in programmed cell death positive regulation of mitochondrial membrane permeability involved in apoptotic process positive regulation of mitochondrial membrane permeability positive regulation of membrane permeability positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway regulation of mitochondrial membrane permeability positive regulation of transport regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway regulation of membrane permeability regulation of mitochondrial membrane permeability involved in apoptotic process mitochondrial outer membrane permeabilization positive regulation of synaptic vesicle recycling positive regulation of endocytosis positive regulation of synaptic vesicle endocytosis Golgi organization regulation of cell differentiation regulation of neuron maturation regulation of cell development cell maturation regulation of cell maturation developmental maturation anatomical structure maturation neuron maturation regulation of neuron differentiation spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation Wnt signalosome assembly protein-containing complex organization protein-containing complex assembly negative regulation of neuron projection development negative regulation of hydrolase activity negative regulation of GTPase activity regulation of catalytic activity negative regulation of molecular function negative regulation of catalytic activity regulation of GTPase activity regulation of molecular function regulation of hydrolase activity regulation of kidney size renal system development kidney morphogenesis animal organ morphogenesis kidney development regulation of anatomical structure size protein autophosphorylation vesicle localization establishment of organelle localization establishment of vesicle localization regulation of synaptic vesicle transport synaptic vesicle localization synaptic vesicle transport regulation of macrophage activation regulation of defense response positive regulation of macrophage activation regulation of response to external stimulus regulation of leukocyte activation positive regulation of microglial cell activation regulation of cell activation positive regulation of neuroinflammatory response myeloid leukocyte activation leukocyte activation macrophage activation positive regulation of cell activation positive regulation of response to external stimulus positive regulation of inflammatory response leukocyte activation involved in inflammatory response regulation of neuroinflammatory response positive regulation of leukocyte activation regulation of immune system process positive regulation of immune system process defense response cell activation response to external stimulus regulation of inflammatory response immune system process positive regulation of defense response microglial cell activation inflammatory response glial cell activation regulation of microglial cell activation neuroinflammatory response regulation of protein stability response to ketone response to curcumin cellular response to ether response to ether cellular response to curcumin cellular response to ketone striatum development subpallium development regulated exocytosis modulation of chemical synaptic transmission synaptic vesicle exocytosis regulation of regulated secretory pathway regulation of secretion by cell secretion by cell signal release neurotransmitter secretion secretion regulation of neurotransmitter transport regulation of synaptic vesicle exocytosis export from cell neurotransmitter transport regulation of secretion signal release from synapse regulation of trans-synaptic signaling exocytosis regulation of neurotransmitter secretion regulation of exocytosis mitochondrion distribution intracellular distribution of mitochondria neuromuscular junction development membrane fusion organelle membrane fusion vesicle organization regulation of protein-containing complex assembly SNARE complex assembly membrane organization organelle fusion regulation of SNARE complex assembly vesicle fusion lysosome organization lytic vacuole organization regulation of mitochondrial depolarization mitochondrial depolarization regulation of membrane depolarization regulation of mitochondrial membrane potential membrane depolarization positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade determination of adult lifespan response to reactive oxygen species cellular response to reactive oxygen species late endosome to lysosome transport negative regulation of transport lysosomal transport negative regulation of late endosome to lysosome transport negative regulation of intracellular transport negative regulation of vacuolar transport regulation of vacuolar transport vacuolar transport regulation of late endosome to lysosome transport regulation of system process modulation of excitatory postsynaptic potential regulation of nervous system process negative regulation of excitatory postsynaptic potential synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic neuron projection arborization reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process neuroblast proliferation cell population proliferation regulation of neuroblast proliferation regulation of cell population proliferation neural precursor cell proliferation regulation of neural precursor cell proliferation regulation of locomotion locomotion	somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle Golgi membrane Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system somatodendritic compartment cell body cellular anatomical structure perikaryon neuronal cell body intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle Golgi membrane Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle organelle organelle membrane amphisome vacuole autophagosome membrane microdomain cell periphery membrane raft caveola neck plasma membrane raft plasma membrane plasma membrane region caveola autolysosome lytic vacuole secondary lysosome lysosome mitochondrial membrane organelle inner membrane mitochondrion mitochondrial inner membrane organelle envelope mitochondrial envelope presynapse presynaptic cytosol synapse cell junction intracellular vesicle phagocytic vesicle cytoplasmic vesicle vesicle endocytic vesicle neuron projection cytoplasm neuron projection plasma membrane bounded cell projection dendrite cytoplasm cell projection dendrite dendritic tree organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane endosome inclusion body Lewy body protein-containing complex ribonucleoprotein complex membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen multivesicular body, internal vesicle endosomal intralumenal vesicle late endosome multivesicular body extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle glutamatergic synapse endoplasmic reticulum exit site Golgi apparatus subcompartment trans-Golgi network cytoskeleton membraneless organelle intracellular membraneless organelle actin cytoskeleton actin-based cell projection microvillus organelle outer membrane mitochondrial outer membrane outer membrane transport vesicle membrane vesicle membrane synaptic vesicle synaptic vesicle membrane transport vesicle exocytic vesicle membrane cytoplasmic vesicle membrane secretory vesicle exocytic vesicle axon postsynapse axon terminus distal axon terminal bouton neuron projection terminus Golgi-associated vesicle cytoplasmic side of membrane cytoplasmic side of mitochondrial outer membrane side of membrane growth cone site of polarized growth Wnt signalosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR032171	C-terminal of Roc, COR-A domain	Domain
A [auth B]	IPR016024	Armadillo-type fold	Homologous Superfamily
A [auth B]	IPR000719	Protein kinase domain	Domain
A [auth B]	IPR020859	Roc domain	Domain
A [auth B]	IPR017441	Protein kinase, ATP binding site	Binding Site
A [auth B]	IPR056597	LRRK2, ARM repeat domain	Domain
A [auth B]	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A [auth B]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A [auth B]	IPR056593	LRRK2, ANK repeat domain	Domain
A [auth B]	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A [auth B]	IPR008271	Serine/threonine-protein kinase, active site	Active Site
A [auth B]	IPR051420	Ser/Thr Protein Kinases with Diverse Regulatory Roles	Family
A [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth B]	IPR001611	Leucine-rich repeat	Repeat
A [auth B]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A [auth B]	IPR056602	LRRK2, beta-propeller	Domain
A [auth B]	IPR003591	Leucine-rich repeat, typical subtype	Repeat
A [auth B]	IPR011989	Armadillo-like helical	Homologous Superfamily
A [auth B]	IPR005225	Small GTP-binding domain	Domain
A [auth B]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A [auth B]	IPR057263	C-terminal of Roc, COR-B domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B]	: Q5S007	Parkinson disease autosomal dominant Parkinson disease 8 renal cell carcinoma sarcomatoid renal cell carcinoma endometriosis collecting duct carcinoma Crohn disease Nerve Degeneration papillary renal cell carcinoma chromophobe renal cell carcinoma inflammatory bowel disease tuberculosis large cell medulloblastoma lung carcinoma multiple system atrophy Parkinson disease autosomal dominant Parkinson disease 8 renal cell carcinoma sarcomatoid renal cell carcinoma endometriosis collecting duct carcinoma Crohn disease Nerve Degeneration papillary renal cell carcinoma chromophobe renal cell carcinoma inflammatory bowel disease tuberculosis large cell medulloblastoma lung carcinoma multiple system atrophy neurodegenerative disease Alzheimer disease ovarian cancer pancreatic intraductal papillary-mucinous carcinoma autosomal recessive juvenile Parkinson disease 2 clear cell renal carcinoma Pick disease renal carcinoma schizophrenia intellectual disability ulcerative colitis late-onset Parkinson disease MALT lymphoma myopathy non-small cell lung carcinoma atypical teratoid rhabdoid tumor ovarian mucinous adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia parkinsonian disorder pilocytic astrocytoma diabetes mellitus thrombocytopenia due to immune destruction invasive ductal breast carcinoma lung adenocarcinoma medulloblastoma osteosarcoma ovarian serous adenocarcinoma common variable immunodeficiency dementia

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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.

9OYA | pdb_00009oya

Full LRRK2 (R1441C mutant) after symmetry expansion

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Pharos: Disease Associations Pharos Homepage Annotation