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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
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
A0009896biological_processpositive regulation of catabolic 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
A0016607cellular_componentnuclear speck
A0016740molecular_functiontransferase activity
A0019005cellular_componentSCF ubiquitin ligase complex
A0019899molecular_functionenzyme binding
A0019900molecular_functionkinase binding
A0019901molecular_functionprotein kinase binding
A0022603biological_processregulation of anatomical structure morphogenesis
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
A0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
A0032991cellular_componentprotein-containing complex
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
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
A0043524biological_processnegative regulation of neuron apoptotic process
A0043653biological_processmitochondrial fragmentation involved in apoptotic process
A0044828biological_processhost-mediated suppression 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
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
A0080090biological_processregulation of primary metabolic process
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
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
A1903530biological_processregulation of secretion by cell
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
A1905091biological_processpositive regulation of type 2 mitophagy
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
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
B0009896biological_processpositive regulation of catabolic 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
B0016607cellular_componentnuclear speck
B0016740molecular_functiontransferase activity
B0019005cellular_componentSCF ubiquitin ligase complex
B0019899molecular_functionenzyme binding
B0019900molecular_functionkinase binding
B0019901molecular_functionprotein kinase binding
B0022603biological_processregulation of anatomical structure morphogenesis
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
B0032436biological_processpositive regulation of proteasomal ubiquitin-dependent protein catabolic process
B0032991cellular_componentprotein-containing complex
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
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
B0043524biological_processnegative regulation of neuron apoptotic process
B0043653biological_processmitochondrial fragmentation involved in apoptotic process
B0044828biological_processhost-mediated suppression 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
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
B0080090biological_processregulation of primary metabolic process
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
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
B1903530biological_processregulation of secretion by cell
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
B1905091biological_processpositive regulation of type 2 mitophagy
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
DetailsZinc finger: {"description":"RING-type 0; atypical"}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues110
DetailsZinc finger: {"description":"RING-type 1","evidences":[{"source":"PROSITE-ProRule","id":"PRU01221","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues62
DetailsZinc finger: {"description":"RING-type 2; atypical","evidences":[{"source":"PROSITE-ProRule","id":"PRU01221","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues68
DetailsRegion: {"description":"SYT11 binding 1","evidences":[{"source":"UniProtKB","id":"O60260","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues72
DetailsRegion: {"description":"SYT11 binding 2","evidences":[{"source":"UniProtKB","id":"O60260","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues2
DetailsActive site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01221","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"23661642","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues48
DetailsBinding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01221","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine; by PINK1","evidences":[{"source":"UniProtKB","id":"O60260","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues2
DetailsModified residue: {"description":"Phosphothreonine; by PINK1","evidences":[{"source":"UniProtKB","id":"O60260","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues2
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"O60260","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI11
Number of Residues5
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ISG15)","evidences":[{"source":"UniProtKB","id":"O60260","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

242500

PDB entries from 2025-10-01

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