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4ZYN

Crystal Structure of Parkin E3 ubiquitin ligase (linker deletion; delta 86-130)

Functional Information from GO Data
ChainGOidnamespacecontents
A0000122biological_processnegative regulation of transcription by RNA polymerase II
A0000139cellular_componentGolgi membrane
A0000151cellular_componentubiquitin ligase complex
A0000209biological_processprotein polyubiquitination
A0000266biological_processmitochondrial fission
A0000422biological_processautophagy of mitochondrion
A0000423biological_processmitophagy
A0001664molecular_functionG protein-coupled receptor binding
A0001933biological_processnegative regulation of protein phosphorylation
A0001963biological_processsynaptic transmission, dopaminergic
A0001964biological_processstartle response
A0003714molecular_functiontranscription corepressor activity
A0003779molecular_functionactin binding
A0004842molecular_functionubiquitin-protein transferase activity
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005741cellular_componentmitochondrial outer membrane
A0005783cellular_componentendoplasmic reticulum
A0005789cellular_componentendoplasmic reticulum membrane
A0005794cellular_componentGolgi apparatus
A0005829cellular_componentcytosol
A0006511biological_processubiquitin-dependent protein catabolic process
A0006513biological_processprotein monoubiquitination
A0006914biological_processautophagy
A0006979biological_processresponse to oxidative stress
A0006986biological_processresponse to unfolded protein
A0007005biological_processmitochondrion organization
A0007612biological_processlearning
A0007626biological_processlocomotory behavior
A0008013molecular_functionbeta-catenin binding
A0008021cellular_componentsynaptic vesicle
A0008270molecular_functionzinc ion binding
A0008344biological_processadult locomotory behavior
A0009410biological_processresponse to xenobiotic stimulus
A0009893biological_processpositive regulation of metabolic process
A0010498biological_processproteasomal protein catabolic process
A0010506biological_processregulation of autophagy
A0010628biological_processpositive regulation of gene expression
A0010629biological_processnegative regulation of gene expression
A0010636biological_processpositive regulation of mitochondrial fusion
A0010637biological_processnegative regulation of mitochondrial fusion
A0010821biological_processregulation of mitochondrion organization
A0010918biological_processpositive regulation of mitochondrial membrane potential
A0010994biological_processfree ubiquitin chain polymerization
A0014069cellular_componentpostsynaptic density
A0014850biological_processresponse to muscle activity
A0015631molecular_functiontubulin binding
A0016235cellular_componentaggresome
A0016567biological_processprotein ubiquitination
A0016740molecular_functiontransferase activity
A0019005cellular_componentSCF ubiquitin ligase complex
A0019899molecular_functionenzyme binding
A0019900molecular_functionkinase binding
A0019901molecular_functionprotein kinase binding
A0030163biological_processprotein catabolic process
A0030165molecular_functionPDZ domain binding
A0030424cellular_componentaxon
A0030544molecular_functionHsp70 protein binding
A0030672cellular_componentsynaptic vesicle membrane
A0031072molecular_functionheat shock protein binding
A0031396biological_processregulation of protein ubiquitination
A0031624molecular_functionubiquitin conjugating enzyme binding
A0031625molecular_functionubiquitin protein ligase binding
A0031647biological_processregulation of protein stability
A0031648biological_processprotein destabilization
A0032232biological_processnegative regulation of actin filament bundle assembly
A0032991cellular_componentprotein-containing complex
A0033132biological_processnegative regulation of glucokinase activity
A0034599biological_processcellular response to oxidative stress
A0034976biological_processresponse to endoplasmic reticulum stress
A0035249biological_processsynaptic transmission, glutamatergic
A0035774biological_processpositive regulation of insulin secretion involved in cellular response to glucose stimulus
A0042053biological_processregulation of dopamine metabolic process
A0042415biological_processnorepinephrine metabolic process
A0042417biological_processdopamine metabolic process
A0042802molecular_functionidentical protein binding
A0042826molecular_functionhistone deacetylase binding
A0042981biological_processregulation of apoptotic process
A0042995cellular_componentcell projection
A0043005cellular_componentneuron projection
A0043025cellular_componentneuronal cell body
A0043065biological_processpositive regulation of apoptotic process
A0043123biological_processpositive regulation of canonical NF-kappaB signal transduction
A0043130molecular_functionubiquitin binding
A0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
A0043195cellular_componentterminal bouton
A0043274molecular_functionphospholipase binding
A0043388biological_processpositive regulation of DNA binding
A0043524biological_processnegative regulation of neuron apoptotic process
A0043653biological_processmitochondrial fragmentation involved in apoptotic process
A0044828biological_processnegative regulation by host of viral genome replication
A0044877molecular_functionprotein-containing complex binding
A0045202cellular_componentsynapse
A0045944biological_processpositive regulation of transcription by RNA polymerase II
A0046329biological_processnegative regulation of JNK cascade
A0046676biological_processnegative regulation of insulin secretion
A0046872molecular_functionmetal ion binding
A0046928biological_processregulation of neurotransmitter secretion
A0048471cellular_componentperinuclear region of cytoplasm
A0050804biological_processmodulation of chemical synaptic transmission
A0050821biological_processprotein stabilization
A0051087molecular_functionprotein-folding chaperone binding
A0051412biological_processresponse to corticosterone
A0051582biological_processpositive regulation of neurotransmitter uptake
A0051583biological_processdopamine uptake involved in synaptic transmission
A0051646biological_processmitochondrion localization
A0051865biological_processprotein autoubiquitination
A0051881biological_processregulation of mitochondrial membrane potential
A0051967biological_processnegative regulation of synaptic transmission, glutamatergic
A0055069biological_processobsolete zinc ion homeostasis
A0061630molecular_functionubiquitin protein ligase activity
A0061734biological_processtype 2 mitophagy
A0070050biological_processneuron cellular homeostasis
A0070534biological_processprotein K63-linked ubiquitination
A0070585biological_processprotein localization to mitochondrion
A0070842biological_processaggresome assembly
A0070936biological_processprotein K48-linked ubiquitination
A0070979biological_processprotein K11-linked ubiquitination
A0071287biological_processcellular response to manganese ion
A0085020biological_processprotein K6-linked ubiquitination
A0090090biological_processnegative regulation of canonical Wnt signaling pathway
A0090141biological_processpositive regulation of mitochondrial fission
A0090201biological_processnegative regulation of release of cytochrome c from mitochondria
A0090258biological_processnegative regulation of mitochondrial fission
A0090394biological_processnegative regulation of excitatory postsynaptic potential
A0097237biological_processcellular response to toxic substance
A0097602molecular_functioncullin family protein binding
A0097708cellular_componentintracellular vesicle
A0098691cellular_componentdopaminergic synapse
A0098779biological_processobsolete positive regulation of mitophagy in response to mitochondrial depolarization
A0098793cellular_componentpresynapse
A0098794cellular_componentpostsynapse
A0098978cellular_componentglutamatergic synapse
A0099072biological_processregulation of postsynaptic membrane neurotransmitter receptor levels
A0099073cellular_componentmitochondrion-derived vesicle
A0099074biological_processmitochondrion to lysosome vesicle-mediated transport
A0140251biological_processregulation protein catabolic process at presynapse
A1900242biological_processregulation of synaptic vesicle endocytosis
A1900407biological_processregulation of cellular response to oxidative stress
A1901526biological_processpositive regulation of mitophagy
A1901800biological_processpositive regulation of proteasomal protein catabolic process
A1902236biological_processnegative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
A1902254biological_processnegative regulation of intrinsic apoptotic signaling pathway by p53 class mediator
A1902530biological_processpositive regulation of protein linear polyubiquitination
A1903265biological_processpositive regulation of tumor necrosis factor-mediated signaling pathway
A1903377biological_processnegative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway
A1903382biological_processnegative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway
A1903427biological_processnegative regulation of reactive oxygen species biosynthetic process
A1903542biological_processnegative regulation of exosomal secretion
A1903861biological_processpositive regulation of dendrite extension
A1904049biological_processnegative regulation of spontaneous neurotransmitter secretion
A1904643biological_processresponse to curcumin
A1904845biological_processcellular response to L-glutamine
A1904881biological_processcellular response to hydrogen sulfide
A1905232biological_processcellular response to L-glutamate
A1905366biological_processnegative regulation of intralumenal vesicle formation
A1905477biological_processpositive regulation of protein localization to membrane
A1990381molecular_functionubiquitin-specific protease binding
A1990444molecular_functionF-box domain binding
A1990452cellular_componentParkin-FBXW7-Cul1 ubiquitin ligase complex
A2000377biological_processregulation of reactive oxygen species metabolic process
A2000378biological_processnegative regulation of reactive oxygen species metabolic process
A2001171biological_processpositive regulation of ATP biosynthetic process
B0000122biological_processnegative regulation of transcription by RNA polymerase II
B0000139cellular_componentGolgi membrane
B0000151cellular_componentubiquitin ligase complex
B0000209biological_processprotein polyubiquitination
B0000266biological_processmitochondrial fission
B0000422biological_processautophagy of mitochondrion
B0000423biological_processmitophagy
B0001664molecular_functionG protein-coupled receptor binding
B0001933biological_processnegative regulation of protein phosphorylation
B0001963biological_processsynaptic transmission, dopaminergic
B0001964biological_processstartle response
B0003714molecular_functiontranscription corepressor activity
B0003779molecular_functionactin binding
B0004842molecular_functionubiquitin-protein transferase activity
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0005741cellular_componentmitochondrial outer membrane
B0005783cellular_componentendoplasmic reticulum
B0005789cellular_componentendoplasmic reticulum membrane
B0005794cellular_componentGolgi apparatus
B0005829cellular_componentcytosol
B0006511biological_processubiquitin-dependent protein catabolic process
B0006513biological_processprotein monoubiquitination
B0006914biological_processautophagy
B0006979biological_processresponse to oxidative stress
B0006986biological_processresponse to unfolded protein
B0007005biological_processmitochondrion organization
B0007612biological_processlearning
B0007626biological_processlocomotory behavior
B0008013molecular_functionbeta-catenin binding
B0008021cellular_componentsynaptic vesicle
B0008270molecular_functionzinc ion binding
B0008344biological_processadult locomotory behavior
B0009410biological_processresponse to xenobiotic stimulus
B0009893biological_processpositive regulation of metabolic process
B0010498biological_processproteasomal protein catabolic process
B0010506biological_processregulation of autophagy
B0010628biological_processpositive regulation of gene expression
B0010629biological_processnegative regulation of gene expression
B0010636biological_processpositive regulation of mitochondrial fusion
B0010637biological_processnegative regulation of mitochondrial fusion
B0010821biological_processregulation of mitochondrion organization
B0010918biological_processpositive regulation of mitochondrial membrane potential
B0010994biological_processfree ubiquitin chain polymerization
B0014069cellular_componentpostsynaptic density
B0014850biological_processresponse to muscle activity
B0015631molecular_functiontubulin binding
B0016235cellular_componentaggresome
B0016567biological_processprotein ubiquitination
B0016740molecular_functiontransferase activity
B0019005cellular_componentSCF ubiquitin ligase complex
B0019899molecular_functionenzyme binding
B0019900molecular_functionkinase binding
B0019901molecular_functionprotein kinase binding
B0030163biological_processprotein catabolic process
B0030165molecular_functionPDZ domain binding
B0030424cellular_componentaxon
B0030544molecular_functionHsp70 protein binding
B0030672cellular_componentsynaptic vesicle membrane
B0031072molecular_functionheat shock protein binding
B0031396biological_processregulation of protein ubiquitination
B0031624molecular_functionubiquitin conjugating enzyme binding
B0031625molecular_functionubiquitin protein ligase binding
B0031647biological_processregulation of protein stability
B0031648biological_processprotein destabilization
B0032232biological_processnegative regulation of actin filament bundle assembly
B0032991cellular_componentprotein-containing complex
B0033132biological_processnegative regulation of glucokinase activity
B0034599biological_processcellular response to oxidative stress
B0034976biological_processresponse to endoplasmic reticulum stress
B0035249biological_processsynaptic transmission, glutamatergic
B0035774biological_processpositive regulation of insulin secretion involved in cellular response to glucose stimulus
B0042053biological_processregulation of dopamine metabolic process
B0042415biological_processnorepinephrine metabolic process
B0042417biological_processdopamine metabolic process
B0042802molecular_functionidentical protein binding
B0042826molecular_functionhistone deacetylase binding
B0042981biological_processregulation of apoptotic process
B0042995cellular_componentcell projection
B0043005cellular_componentneuron projection
B0043025cellular_componentneuronal cell body
B0043065biological_processpositive regulation of apoptotic process
B0043123biological_processpositive regulation of canonical NF-kappaB signal transduction
B0043130molecular_functionubiquitin binding
B0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
B0043195cellular_componentterminal bouton
B0043274molecular_functionphospholipase binding
B0043388biological_processpositive regulation of DNA binding
B0043524biological_processnegative regulation of neuron apoptotic process
B0043653biological_processmitochondrial fragmentation involved in apoptotic process
B0044828biological_processnegative regulation by host of viral genome replication
B0044877molecular_functionprotein-containing complex binding
B0045202cellular_componentsynapse
B0045944biological_processpositive regulation of transcription by RNA polymerase II
B0046329biological_processnegative regulation of JNK cascade
B0046676biological_processnegative regulation of insulin secretion
B0046872molecular_functionmetal ion binding
B0046928biological_processregulation of neurotransmitter secretion
B0048471cellular_componentperinuclear region of cytoplasm
B0050804biological_processmodulation of chemical synaptic transmission
B0050821biological_processprotein stabilization
B0051087molecular_functionprotein-folding chaperone binding
B0051412biological_processresponse to corticosterone
B0051582biological_processpositive regulation of neurotransmitter uptake
B0051583biological_processdopamine uptake involved in synaptic transmission
B0051646biological_processmitochondrion localization
B0051865biological_processprotein autoubiquitination
B0051881biological_processregulation of mitochondrial membrane potential
B0051967biological_processnegative regulation of synaptic transmission, glutamatergic
B0055069biological_processobsolete zinc ion homeostasis
B0061630molecular_functionubiquitin protein ligase activity
B0061734biological_processtype 2 mitophagy
B0070050biological_processneuron cellular homeostasis
B0070534biological_processprotein K63-linked ubiquitination
B0070585biological_processprotein localization to mitochondrion
B0070842biological_processaggresome assembly
B0070936biological_processprotein K48-linked ubiquitination
B0070979biological_processprotein K11-linked ubiquitination
B0071287biological_processcellular response to manganese ion
B0085020biological_processprotein K6-linked ubiquitination
B0090090biological_processnegative regulation of canonical Wnt signaling pathway
B0090141biological_processpositive regulation of mitochondrial fission
B0090201biological_processnegative regulation of release of cytochrome c from mitochondria
B0090258biological_processnegative regulation of mitochondrial fission
B0090394biological_processnegative regulation of excitatory postsynaptic potential
B0097237biological_processcellular response to toxic substance
B0097602molecular_functioncullin family protein binding
B0097708cellular_componentintracellular vesicle
B0098691cellular_componentdopaminergic synapse
B0098779biological_processobsolete positive regulation of mitophagy in response to mitochondrial depolarization
B0098793cellular_componentpresynapse
B0098794cellular_componentpostsynapse
B0098978cellular_componentglutamatergic synapse
B0099072biological_processregulation of postsynaptic membrane neurotransmitter receptor levels
B0099073cellular_componentmitochondrion-derived vesicle
B0099074biological_processmitochondrion to lysosome vesicle-mediated transport
B0140251biological_processregulation protein catabolic process at presynapse
B1900242biological_processregulation of synaptic vesicle endocytosis
B1900407biological_processregulation of cellular response to oxidative stress
B1901526biological_processpositive regulation of mitophagy
B1901800biological_processpositive regulation of proteasomal protein catabolic process
B1902236biological_processnegative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
B1902254biological_processnegative regulation of intrinsic apoptotic signaling pathway by p53 class mediator
B1902530biological_processpositive regulation of protein linear polyubiquitination
B1903265biological_processpositive regulation of tumor necrosis factor-mediated signaling pathway
B1903377biological_processnegative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway
B1903382biological_processnegative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway
B1903427biological_processnegative regulation of reactive oxygen species biosynthetic process
B1903542biological_processnegative regulation of exosomal secretion
B1903861biological_processpositive regulation of dendrite extension
B1904049biological_processnegative regulation of spontaneous neurotransmitter secretion
B1904643biological_processresponse to curcumin
B1904845biological_processcellular response to L-glutamine
B1904881biological_processcellular response to hydrogen sulfide
B1905232biological_processcellular response to L-glutamate
B1905366biological_processnegative regulation of intralumenal vesicle formation
B1905477biological_processpositive regulation of protein localization to membrane
B1990381molecular_functionubiquitin-specific protease binding
B1990444molecular_functionF-box domain binding
B1990452cellular_componentParkin-FBXW7-Cul1 ubiquitin ligase complex
B2000377biological_processregulation of reactive oxygen species metabolic process
B2000378biological_processnegative regulation of reactive oxygen species metabolic process
B2001171biological_processpositive regulation of ATP biosynthetic process
Functional Information from PDB Data
site_idAC1
Number of Residues4
Detailsbinding site for residue ZN A 501
ChainResidue
ACYS150
ACYS154
ACYS212
AHIS215

site_idAC2
Number of Residues4
Detailsbinding site for residue ZN A 502
ChainResidue
ACYS166
ACYS169
ACYS196
ACYS201

site_idAC3
Number of Residues4
Detailsbinding site for residue ZN A 503
ChainResidue
ACYS241
ACYS260
ACYS263
ACYS238

site_idAC4
Number of Residues4
Detailsbinding site for residue ZN A 504
ChainResidue
ACYS253
AHIS257
ACYS289
ACYS293

site_idAC5
Number of Residues5
Detailsbinding site for residue ZN A 505
ChainResidue
ACYS332
AARG334
ACYS337
ACYS352
ACYS360

site_idAC6
Number of Residues4
Detailsbinding site for residue ZN A 506
ChainResidue
ACYS365
ACYS368
AHIS373
ACYS377

site_idAC7
Number of Residues4
Detailsbinding site for residue ZN A 507
ChainResidue
ACYS418
ACYS421
ACYS436
ACYS441

site_idAC8
Number of Residues4
Detailsbinding site for residue ZN A 508
ChainResidue
ACYS446
ACYS449
ACYS457
AHIS461

site_idAC9
Number of Residues3
Detailsbinding site for residue SO4 A 509
ChainResidue
AARG305
ATYR312
AARG420

site_idAD1
Number of Residues5
Detailsbinding site for residue SO4 A 510
ChainResidue
AARG163
ASER218
AASP221
AARG455
ASO4512

site_idAD2
Number of Residues2
Detailsbinding site for residue SO4 A 511
ChainResidue
AARG245
AHOH617

site_idAD3
Number of Residues6
Detailsbinding site for residue SO4 A 512
ChainResidue
ALYS161
AARG163
ALYS211
ATHR217
ASER218
ASO4510

site_idAD4
Number of Residues4
Detailsbinding site for residue ZN B 501
ChainResidue
BCYS150
BCYS154
BCYS212
BHIS215

site_idAD5
Number of Residues4
Detailsbinding site for residue ZN B 502
ChainResidue
BCYS166
BCYS169
BCYS196
BCYS201

site_idAD6
Number of Residues4
Detailsbinding site for residue ZN B 503
ChainResidue
BCYS238
BCYS241
BCYS260
BCYS263

site_idAD7
Number of Residues4
Detailsbinding site for residue ZN B 504
ChainResidue
BCYS253
BHIS257
BCYS289
BCYS293

site_idAD8
Number of Residues4
Detailsbinding site for residue ZN B 505
ChainResidue
BCYS332
BCYS337
BCYS352
BCYS360

site_idAD9
Number of Residues5
Detailsbinding site for residue ZN B 506
ChainResidue
BCYS365
BASP367
BCYS368
BHIS373
BCYS377

site_idAE1
Number of Residues4
Detailsbinding site for residue ZN B 507
ChainResidue
BCYS418
BCYS421
BCYS436
BCYS441

site_idAE2
Number of Residues4
Detailsbinding site for residue ZN B 508
ChainResidue
BCYS446
BCYS449
BCYS457
BHIS461

site_idAE3
Number of Residues3
Detailsbinding site for residue SO4 B 509
ChainResidue
BARG305
BTYR312
BARG420

site_idAE4
Number of Residues4
Detailsbinding site for residue SO4 B 510
ChainResidue
BLYS161
BARG163
BLYS211
BSER218

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues168
DetailsZN_FING: RING-type 0; atypical
ChainResidueDetails
AVAL186-THR270
BVAL186-THR270

site_idSWS_FT_FI2
Number of Residues110
DetailsZN_FING: RING-type 1 => ECO:0000255|PROSITE-ProRule:PRU01221
ChainResidueDetails
ALEU283-GLY338
BLEU283-GLY338

site_idSWS_FT_FI3
Number of Residues128
DetailsZN_FING: IBR-type => ECO:0000255|PROSITE-ProRule:PRU01221
ChainResidueDetails
ALEU358-ASN422
BLEU358-ASN422

site_idSWS_FT_FI4
Number of Residues62
DetailsZN_FING: RING-type 2; atypical => ECO:0000255|PROSITE-ProRule:PRU01221
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues2
DetailsACT_SITE: ACT_SITE => ECO:0000255|PROSITE-ProRule:PRU01221, ECO:0000269|PubMed:23661642
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues48
DetailsBINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU01221
ChainResidueDetails
ALEU283
AGLU382
AALA397
AGLU405
ATHR410
ALYS413
ACYS418
AASN422
APHE463
ASER286
BLEU283
BSER286
BILE298
BHIS302
BARG305
AILE298
BGLY308
BARG334
BGLY338
BCYS377
BGLU382
BALA397
BGLU405
BTHR410
BLYS413
BCYS418
AHIS302
BASN422
BPHE463
AARG305
AGLY308
AARG334
AGLY338
ACYS377

site_idSWS_FT_FI7
Number of Residues2
DetailsMOD_RES: Phosphoserine; by PINK1 => ECO:0000250|UniProtKB:O60260
ChainResidueDetails
ASER65
BSER65

site_idSWS_FT_FI8
Number of Residues2
DetailsMOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q9WVS6
ChainResidueDetails
ATHR125
BTHR125

site_idSWS_FT_FI9
Number of Residues2
DetailsMOD_RES: Phosphothreonine; by PINK1 => ECO:0000250|UniProtKB:O60260
ChainResidueDetails
ALYS220
BLYS220

site_idSWS_FT_FI10
Number of Residues2
DetailsMOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:O60260
ChainResidueDetails
AASP262
BASP262

site_idSWS_FT_FI11
Number of Residues6
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ISG15) => ECO:0000250|UniProtKB:O60260
ChainResidueDetails
AASP394
ATHR414
BASP394
BTHR414

226707

PDB entries from 2024-10-30

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