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8U8B

Cryo-EM structure of LRRK2 bound to type II inhibitor rebastinib

Functional Information from GO Data
ChainGOidnamespacecontents
A0000139cellular_componentGolgi membrane
A0000149molecular_functionSNARE binding
A0000165biological_processMAPK cascade
A0000287molecular_functionmagnesium ion binding
A0001933biological_processnegative regulation of protein phosphorylation
A0001934biological_processpositive regulation of protein phosphorylation
A0003779molecular_functionactin binding
A0003924molecular_functionGTPase activity
A0004672molecular_functionprotein kinase activity
A0004674molecular_functionprotein serine/threonine kinase activity
A0004706molecular_functionJUN kinase kinase kinase activity
A0004709molecular_functionMAP kinase kinase kinase activity
A0005096molecular_functionGTPase activator activity
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005525molecular_functionGTP binding
A0005615cellular_componentextracellular space
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005741cellular_componentmitochondrial outer membrane
A0005743cellular_componentmitochondrial inner membrane
A0005759cellular_componentmitochondrial matrix
A0005764cellular_componentlysosome
A0005768cellular_componentendosome
A0005783cellular_componentendoplasmic reticulum
A0005789cellular_componentendoplasmic reticulum membrane
A0005794cellular_componentGolgi apparatus
A0005798cellular_componentGolgi-associated vesicle
A0005802cellular_componenttrans-Golgi network
A0005829cellular_componentcytosol
A0005856cellular_componentcytoskeleton
A0005886cellular_componentplasma membrane
A0005902cellular_componentmicrovillus
A0006468biological_processprotein phosphorylation
A0006606biological_processprotein import into nucleus
A0006897biological_processendocytosis
A0006914biological_processautophagy
A0006979biological_processresponse to oxidative stress
A0007005biological_processmitochondrion organization
A0007029biological_processendoplasmic reticulum organization
A0007030biological_processGolgi organization
A0007040biological_processlysosome organization
A0007165biological_processsignal transduction
A0007254biological_processJNK cascade
A0007266biological_processRho protein signal transduction
A0007283biological_processspermatogenesis
A0007528biological_processneuromuscular junction development
A0008017molecular_functionmicrotubule binding
A0008021cellular_componentsynaptic vesicle
A0008104biological_processprotein localization
A0008340biological_processdetermination of adult lifespan
A0009267biological_processcellular response to starvation
A0009966biological_processregulation of signal transduction
A0010468biological_processregulation of gene expression
A0010506biological_processregulation of autophagy
A0010508biological_processpositive regulation of autophagy
A0010738biological_processregulation of protein kinase A signaling
A0010955biological_processnegative regulation of protein processing
A0010977biological_processnegative regulation of neuron projection development
A0014041biological_processregulation of neuron maturation
A0015631molecular_functiontubulin binding
A0016242biological_processnegative regulation of macroautophagy
A0016301molecular_functionkinase activity
A0016310biological_processphosphorylation
A0016787molecular_functionhydrolase activity
A0017075molecular_functionsyntaxin-1 binding
A0018105biological_processpeptidyl-serine phosphorylation
A0018107biological_processpeptidyl-threonine phosphorylation
A0019722biological_processcalcium-mediated signaling
A0021756biological_processstriatum development
A0021772biological_processolfactory bulb development
A0022028biological_processtangential migration from the subventricular zone to the olfactory bulb
A0030154biological_processcell differentiation
A0030159molecular_functionsignaling receptor complex adaptor activity
A0030276molecular_functionclathrin binding
A0030424cellular_componentaxon
A0030425cellular_componentdendrite
A0030426cellular_componentgrowth cone
A0030672cellular_componentsynaptic vesicle membrane
A0031267molecular_functionsmall GTPase binding
A0031398biological_processpositive regulation of protein ubiquitination
A0031410cellular_componentcytoplasmic vesicle
A0031647biological_processregulation of protein stability
A0031966cellular_componentmitochondrial membrane
A0032091biological_processnegative regulation of protein binding
A0032092biological_processpositive regulation of protein binding
A0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
A0032473cellular_componentcytoplasmic side of mitochondrial outer membrane
A0032760biological_processpositive regulation of tumor necrosis factor production
A0032839cellular_componentdendrite cytoplasm
A0034211molecular_functionGTP-dependent protein kinase activity
A0034260biological_processnegative regulation of GTPase activity
A0034599biological_processcellular response to oxidative stress
A0034614biological_processcellular response to reactive oxygen species
A0035556biological_processintracellular signal transduction
A0035564biological_processregulation of kidney size
A0035640biological_processexploration behavior
A0035641biological_processlocomotory exploration behavior
A0035751biological_processregulation of lysosomal lumen pH
A0036479molecular_functionperoxidase inhibitor activity
A0039706molecular_functionco-receptor binding
A0040012biological_processregulation of locomotion
A0042391biological_processregulation of membrane potential
A0042802molecular_functionidentical protein binding
A0042803molecular_functionprotein homodimerization activity
A0042995cellular_componentcell projection
A0043005cellular_componentneuron projection
A0043025cellular_componentneuronal cell body
A0043068biological_processpositive regulation of programmed cell death
A0043195cellular_componentterminal bouton
A0043204cellular_componentperikaryon
A0043231cellular_componentintracellular membrane-bounded organelle
A0043406biological_processpositive regulation of MAP kinase activity
A0044325molecular_functiontransmembrane transporter binding
A0044753cellular_componentamphisome
A0044754cellular_componentautolysosome
A0045121cellular_componentmembrane raft
A0045202cellular_componentsynapse
A0045860biological_processpositive regulation of protein kinase activity
A0046039biological_processGTP metabolic process
A0046777biological_processprotein autophosphorylation
A0048312biological_processintracellular distribution of mitochondria
A0048812biological_processneuron projection morphogenesis
A0051018molecular_functionprotein kinase A binding
A0051646biological_processmitochondrion localization
A0051770biological_processpositive regulation of nitric-oxide synthase biosynthetic process
A0051900biological_processregulation of mitochondrial depolarization
A0051966biological_processregulation of synaptic transmission, glutamatergic
A0060070biological_processcanonical Wnt signaling pathway
A0060079biological_processexcitatory postsynaptic potential
A0060159biological_processregulation of dopamine receptor signaling pathway
A0060161biological_processpositive regulation of dopamine receptor signaling pathway
A0060628biological_processregulation of ER to Golgi vesicle-mediated transport
A0060828biological_processregulation of canonical Wnt signaling pathway
A0061001biological_processregulation of dendritic spine morphogenesis
A0070062cellular_componentextracellular exosome
A0070585biological_processprotein localization to mitochondrion
A0070971cellular_componentendoplasmic reticulum exit site
A0070973biological_processprotein localization to endoplasmic reticulum exit site
A0071287biological_processcellular response to manganese ion
A0071407biological_processcellular response to organic cyclic compound
A0090140biological_processregulation of mitochondrial fission
A0090263biological_processpositive regulation of canonical Wnt signaling pathway
A0090394biological_processnegative regulation of excitatory postsynaptic potential
A0097487cellular_componentmultivesicular body, internal vesicle
A0098794cellular_componentpostsynapse
A0098978cellular_componentglutamatergic synapse
A0099400cellular_componentcaveola neck
A0099523cellular_componentpresynaptic cytosol
A0106310molecular_functionprotein serine kinase activity
A0140058biological_processneuron projection arborization
A1900242biological_processregulation of synaptic vesicle endocytosis
A1900244biological_processpositive regulation of synaptic vesicle endocytosis
A1902236biological_processnegative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
A1902499biological_processpositive regulation of protein autoubiquitination
A1902692biological_processregulation of neuroblast proliferation
A1902803biological_processregulation of synaptic vesicle transport
A1902823biological_processnegative regulation of late endosome to lysosome transport
A1902902biological_processnegative regulation of autophagosome assembly
A1903125biological_processnegative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation
A1903215biological_processnegative regulation of protein targeting to mitochondrion
A1903217biological_processnegative regulation of protein processing involved in protein targeting to mitochondrion
A1903351biological_processcellular response to dopamine
A1903980biological_processpositive regulation of microglial cell activation
A1904713molecular_functionbeta-catenin destruction complex binding
A1904887biological_processWnt signalosome assembly
A1905279biological_processregulation of retrograde transport, endosome to Golgi
A1905289biological_processregulation of CAMKK-AMPK signaling cascade
A1990904cellular_componentribonucleoprotein complex
A1990909cellular_componentWnt signalosome
A2000172biological_processregulation of branching morphogenesis of a nerve
A2000300biological_processregulation of synaptic vesicle exocytosis
A2000377biological_processregulation of reactive oxygen species metabolic process
B0000139cellular_componentGolgi membrane
B0000149molecular_functionSNARE binding
B0000165biological_processMAPK cascade
B0000287molecular_functionmagnesium ion binding
B0001933biological_processnegative regulation of protein phosphorylation
B0001934biological_processpositive regulation of protein phosphorylation
B0003779molecular_functionactin binding
B0003924molecular_functionGTPase activity
B0004672molecular_functionprotein kinase activity
B0004674molecular_functionprotein serine/threonine kinase activity
B0004706molecular_functionJUN kinase kinase kinase activity
B0004709molecular_functionMAP kinase kinase kinase activity
B0005096molecular_functionGTPase activator activity
B0005515molecular_functionprotein binding
B0005524molecular_functionATP binding
B0005525molecular_functionGTP binding
B0005615cellular_componentextracellular space
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0005741cellular_componentmitochondrial outer membrane
B0005743cellular_componentmitochondrial inner membrane
B0005759cellular_componentmitochondrial matrix
B0005764cellular_componentlysosome
B0005768cellular_componentendosome
B0005783cellular_componentendoplasmic reticulum
B0005789cellular_componentendoplasmic reticulum membrane
B0005794cellular_componentGolgi apparatus
B0005798cellular_componentGolgi-associated vesicle
B0005802cellular_componenttrans-Golgi network
B0005829cellular_componentcytosol
B0005856cellular_componentcytoskeleton
B0005886cellular_componentplasma membrane
B0005902cellular_componentmicrovillus
B0006468biological_processprotein phosphorylation
B0006606biological_processprotein import into nucleus
B0006897biological_processendocytosis
B0006914biological_processautophagy
B0006979biological_processresponse to oxidative stress
B0007005biological_processmitochondrion organization
B0007029biological_processendoplasmic reticulum organization
B0007030biological_processGolgi organization
B0007040biological_processlysosome organization
B0007165biological_processsignal transduction
B0007254biological_processJNK cascade
B0007266biological_processRho protein signal transduction
B0007283biological_processspermatogenesis
B0007528biological_processneuromuscular junction development
B0008017molecular_functionmicrotubule binding
B0008021cellular_componentsynaptic vesicle
B0008104biological_processprotein localization
B0008340biological_processdetermination of adult lifespan
B0009267biological_processcellular response to starvation
B0009966biological_processregulation of signal transduction
B0010468biological_processregulation of gene expression
B0010506biological_processregulation of autophagy
B0010508biological_processpositive regulation of autophagy
B0010738biological_processregulation of protein kinase A signaling
B0010955biological_processnegative regulation of protein processing
B0010977biological_processnegative regulation of neuron projection development
B0014041biological_processregulation of neuron maturation
B0015631molecular_functiontubulin binding
B0016242biological_processnegative regulation of macroautophagy
B0016301molecular_functionkinase activity
B0016310biological_processphosphorylation
B0016787molecular_functionhydrolase activity
B0017075molecular_functionsyntaxin-1 binding
B0018105biological_processpeptidyl-serine phosphorylation
B0018107biological_processpeptidyl-threonine phosphorylation
B0019722biological_processcalcium-mediated signaling
B0021756biological_processstriatum development
B0021772biological_processolfactory bulb development
B0022028biological_processtangential migration from the subventricular zone to the olfactory bulb
B0030154biological_processcell differentiation
B0030159molecular_functionsignaling receptor complex adaptor activity
B0030276molecular_functionclathrin binding
B0030424cellular_componentaxon
B0030425cellular_componentdendrite
B0030426cellular_componentgrowth cone
B0030672cellular_componentsynaptic vesicle membrane
B0031267molecular_functionsmall GTPase binding
B0031398biological_processpositive regulation of protein ubiquitination
B0031410cellular_componentcytoplasmic vesicle
B0031647biological_processregulation of protein stability
B0031966cellular_componentmitochondrial membrane
B0032091biological_processnegative regulation of protein binding
B0032092biological_processpositive regulation of protein binding
B0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
B0032473cellular_componentcytoplasmic side of mitochondrial outer membrane
B0032760biological_processpositive regulation of tumor necrosis factor production
B0032839cellular_componentdendrite cytoplasm
B0034211molecular_functionGTP-dependent protein kinase activity
B0034260biological_processnegative regulation of GTPase activity
B0034599biological_processcellular response to oxidative stress
B0034614biological_processcellular response to reactive oxygen species
B0035556biological_processintracellular signal transduction
B0035564biological_processregulation of kidney size
B0035640biological_processexploration behavior
B0035641biological_processlocomotory exploration behavior
B0035751biological_processregulation of lysosomal lumen pH
B0036479molecular_functionperoxidase inhibitor activity
B0039706molecular_functionco-receptor binding
B0040012biological_processregulation of locomotion
B0042391biological_processregulation of membrane potential
B0042802molecular_functionidentical protein binding
B0042803molecular_functionprotein homodimerization activity
B0042995cellular_componentcell projection
B0043005cellular_componentneuron projection
B0043025cellular_componentneuronal cell body
B0043068biological_processpositive regulation of programmed cell death
B0043195cellular_componentterminal bouton
B0043204cellular_componentperikaryon
B0043231cellular_componentintracellular membrane-bounded organelle
B0043406biological_processpositive regulation of MAP kinase activity
B0044325molecular_functiontransmembrane transporter binding
B0044753cellular_componentamphisome
B0044754cellular_componentautolysosome
B0045121cellular_componentmembrane raft
B0045202cellular_componentsynapse
B0045860biological_processpositive regulation of protein kinase activity
B0046039biological_processGTP metabolic process
B0046777biological_processprotein autophosphorylation
B0048312biological_processintracellular distribution of mitochondria
B0048812biological_processneuron projection morphogenesis
B0051018molecular_functionprotein kinase A binding
B0051646biological_processmitochondrion localization
B0051770biological_processpositive regulation of nitric-oxide synthase biosynthetic process
B0051900biological_processregulation of mitochondrial depolarization
B0051966biological_processregulation of synaptic transmission, glutamatergic
B0060070biological_processcanonical Wnt signaling pathway
B0060079biological_processexcitatory postsynaptic potential
B0060159biological_processregulation of dopamine receptor signaling pathway
B0060161biological_processpositive regulation of dopamine receptor signaling pathway
B0060628biological_processregulation of ER to Golgi vesicle-mediated transport
B0060828biological_processregulation of canonical Wnt signaling pathway
B0061001biological_processregulation of dendritic spine morphogenesis
B0070062cellular_componentextracellular exosome
B0070585biological_processprotein localization to mitochondrion
B0070971cellular_componentendoplasmic reticulum exit site
B0070973biological_processprotein localization to endoplasmic reticulum exit site
B0071287biological_processcellular response to manganese ion
B0071407biological_processcellular response to organic cyclic compound
B0090140biological_processregulation of mitochondrial fission
B0090263biological_processpositive regulation of canonical Wnt signaling pathway
B0090394biological_processnegative regulation of excitatory postsynaptic potential
B0097487cellular_componentmultivesicular body, internal vesicle
B0098794cellular_componentpostsynapse
B0098978cellular_componentglutamatergic synapse
B0099400cellular_componentcaveola neck
B0099523cellular_componentpresynaptic cytosol
B0106310molecular_functionprotein serine kinase activity
B0140058biological_processneuron projection arborization
B1900242biological_processregulation of synaptic vesicle endocytosis
B1900244biological_processpositive regulation of synaptic vesicle endocytosis
B1902236biological_processnegative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
B1902499biological_processpositive regulation of protein autoubiquitination
B1902692biological_processregulation of neuroblast proliferation
B1902803biological_processregulation of synaptic vesicle transport
B1902823biological_processnegative regulation of late endosome to lysosome transport
B1902902biological_processnegative regulation of autophagosome assembly
B1903125biological_processnegative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation
B1903215biological_processnegative regulation of protein targeting to mitochondrion
B1903217biological_processnegative regulation of protein processing involved in protein targeting to mitochondrion
B1903351biological_processcellular response to dopamine
B1903980biological_processpositive regulation of microglial cell activation
B1904713molecular_functionbeta-catenin destruction complex binding
B1904887biological_processWnt signalosome assembly
B1905279biological_processregulation of retrograde transport, endosome to Golgi
B1905289biological_processregulation of CAMKK-AMPK signaling cascade
B1990904cellular_componentribonucleoprotein complex
B1990909cellular_componentWnt signalosome
B2000172biological_processregulation of branching morphogenesis of a nerve
B2000300biological_processregulation of synaptic vesicle exocytosis
B2000377biological_processregulation of reactive oxygen species metabolic process
Functional Information from PROSITE/UniProt
site_idPS00107
Number of Residues22
DetailsPROTEIN_KINASE_ATP Protein kinases ATP-binding region signature. LGDGSFGSVYrAayegee............VAVK
ChainResidueDetails
ALEU1885-LYS1906

site_idPS00108
Number of Residues13
DetailsPROTEIN_KINASE_ST Serine/Threonine protein kinases active-site signature. IiYrDLKphNVLL
ChainResidueDetails
AILE1990-LEU2002

site_idPS00626
Number of Residues11
DetailsRCC1_2 Regulator of chromosome condensation (RCC1) signature 2. IGTGgGHILLL
ChainResidueDetails
AILE2427-LEU2437

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: Proton acceptor => ECO:0000255|PROSITE-ProRule:PRU00159, ECO:0000255|PROSITE-ProRule:PRU10027
ChainResidueDetails
AASP1994
BASP1994

site_idSWS_FT_FI2
Number of Residues2
DetailsBINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00758, ECO:0000269|PubMed:18230735
ChainResidueDetails
AGLY1341
BGLY1341

site_idSWS_FT_FI3
Number of Residues4
DetailsBINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00159
ChainResidueDetails
ALEU1885
ALYS1906
BLEU1885
BLYS1906

site_idSWS_FT_FI4
Number of Residues4
DetailsBINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00758
ChainResidueDetails
AGLU2098
AASN2295
BGLU2098
BASN2295

site_idSWS_FT_FI5
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000269|PubMed:28202711, ECO:0000269|PubMed:28720718, ECO:0000269|PubMed:29212815
ChainResidueDetails
ASER910
BSER910

site_idSWS_FT_FI6
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000269|PubMed:28202711, ECO:0000269|PubMed:28720718, ECO:0000269|PubMed:29127255, ECO:0000269|PubMed:29212815, ECO:0000269|PubMed:30635421
ChainResidueDetails
ASER935
BSER935

site_idSWS_FT_FI7
Number of Residues4
DetailsMOD_RES: Phosphoserine => ECO:0000269|PubMed:28202711, ECO:0000269|PubMed:29212815
ChainResidueDetails
ASER955
ASER973
BSER955
BSER973

site_idSWS_FT_FI8
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000269|PubMed:29212815, ECO:0000269|PubMed:30635421
ChainResidueDetails
ASER1292
BSER1292

site_idSWS_FT_FI9
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000269|PubMed:28202711
ChainResidueDetails
ASER1444
BSER1444

222415

PDB entries from 2024-07-10

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