Structure of PDB 4k95 Chain B Binding Site BS07

Receptor Information
>4k95 Chain B (length=375) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIVFVRFNSSYGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKEL
QNHLTVQNCDLEQQSIVHIVQRPTYHSFFVYCKGPCHKVQPGKLRVQCGT
CRQATLTLAQGPSCWDDVLIPNRMSGECQSPDCPGTRAEFFFKCGAHPTS
DKDTSVALNLITNNSRSIPCIACTDVRNPVLVFQCNHRHVICLDCFHLYC
VTRLNDRQFVHDAQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQY
GAEECVLQMGGVLCPRPGCGAGLLPEQGQRKVTCEGGNGLGCGFVFCRDC
KEAYHEGECDRVDQRAAEQARWETTKPCPRCNVPIEKNGGCMHMKCPQPQ
CKLEWCWNCGCEWNRACMGDHWFDV
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain4k95 Chain B Residue 507 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4k95 Structure of parkin reveals mechanisms for ubiquitin ligase activation.
Resolution6.499 Å
Binding residue
(original residue number in PDB)		C418 C421 C436 C441
Binding residue
(residue number reindexed from 1)		C328 C331 C346 C351
Annotation score4
Enzymatic activity
Enzyme Commision number 2.3.2.31: RBR-type E3 ubiquitin transferase.
Gene Ontology
Molecular Function
GO:0001664 G protein-coupled receptor binding
GO:0003714 transcription corepressor activity
GO:0003779 actin binding
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0008013 beta-catenin binding
GO:0008270 zinc ion binding
GO:0015631 tubulin binding
GO:0016740 transferase activity
GO:0019899 enzyme binding
GO:0019900 kinase binding
GO:0019901 protein kinase binding
GO:0030165 PDZ domain binding
GO:0030544 Hsp70 protein binding
GO:0031072 heat shock protein binding
GO:0031624 ubiquitin conjugating enzyme binding
GO:0031625 ubiquitin protein ligase binding
GO:0042802 identical protein binding
GO:0042826 histone deacetylase binding
GO:0043130 ubiquitin binding
GO:0043274 phospholipase binding
GO:0044877 protein-containing complex binding
GO:0046872 metal ion binding
GO:0051087 protein-folding chaperone binding
GO:0061630 ubiquitin protein ligase activity
GO:0097602 cullin family protein binding
GO:1990381 ubiquitin-specific protease binding
GO:1990444 F-box domain binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0000209 protein polyubiquitination
GO:0000266 mitochondrial fission
GO:0000422 autophagy of mitochondrion
GO:0000423 mitophagy
GO:0001933 negative regulation of protein phosphorylation
GO:0001963 synaptic transmission, dopaminergic
GO:0001964 startle response
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006513 protein monoubiquitination
GO:0006914 autophagy
GO:0006979 response to oxidative stress
GO:0006986 response to unfolded protein
GO:0007005 mitochondrion organization
GO:0007612 learning
GO:0007626 locomotory behavior
GO:0008344 adult locomotory behavior
GO:0009410 response to xenobiotic stimulus
GO:0009893 positive regulation of metabolic process
GO:0010498 proteasomal protein catabolic process
GO:0010506 regulation of autophagy
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0010636 positive regulation of mitochondrial fusion
GO:0010637 negative regulation of mitochondrial fusion
GO:0010821 regulation of mitochondrion organization
GO:0010918 positive regulation of mitochondrial membrane potential
GO:0010994 free ubiquitin chain polymerization
GO:0014850 response to muscle activity
GO:0016567 protein ubiquitination
GO:0030163 protein catabolic process
GO:0031396 regulation of protein ubiquitination
GO:0031647 regulation of protein stability
GO:0031648 protein destabilization
GO:0032232 negative regulation of actin filament bundle assembly
GO:0033132 negative regulation of glucokinase activity
GO:0034599 cellular response to oxidative stress
GO:0034976 response to endoplasmic reticulum stress
GO:0035249 synaptic transmission, glutamatergic
GO:0035774 positive regulation of insulin secretion involved in cellular response to glucose stimulus
GO:0042053 regulation of dopamine metabolic process
GO:0042415 norepinephrine metabolic process
GO:0042417 dopamine metabolic process
GO:0042981 regulation of apoptotic process
GO:0043065 positive regulation of apoptotic process
GO:0043123 positive regulation of canonical NF-kappaB signal transduction
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0043388 positive regulation of DNA binding
GO:0043524 negative regulation of neuron apoptotic process
GO:0043653 mitochondrial fragmentation involved in apoptotic process
GO:0044828 negative regulation by host of viral genome replication
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0046329 negative regulation of JNK cascade
GO:0046676 negative regulation of insulin secretion
GO:0046928 regulation of neurotransmitter secretion
GO:0050804 modulation of chemical synaptic transmission
GO:0050821 protein stabilization
GO:0051412 response to corticosterone
GO:0051582 positive regulation of neurotransmitter uptake
GO:0051583 dopamine uptake involved in synaptic transmission
GO:0051646 mitochondrion localization
GO:0051865 protein autoubiquitination
GO:0051881 regulation of mitochondrial membrane potential
GO:0051967 negative regulation of synaptic transmission, glutamatergic
GO:0061734 type 2 mitophagy
GO:0070050 neuron cellular homeostasis
GO:0070534 protein K63-linked ubiquitination
GO:0070585 protein localization to mitochondrion
GO:0070842 aggresome assembly
GO:0070936 protein K48-linked ubiquitination
GO:0070979 protein K11-linked ubiquitination
GO:0071287 cellular response to manganese ion
GO:0085020 protein K6-linked ubiquitination
GO:0090090 negative regulation of canonical Wnt signaling pathway
GO:0090141 positive regulation of mitochondrial fission
GO:0090201 negative regulation of release of cytochrome c from mitochondria
GO:0090258 negative regulation of mitochondrial fission
GO:0090394 negative regulation of excitatory postsynaptic potential
GO:0097237 cellular response to toxic substance
GO:0099072 regulation of postsynaptic membrane neurotransmitter receptor levels
GO:0099074 mitochondrion to lysosome vesicle-mediated transport
GO:0140251 regulation protein catabolic process at presynapse
GO:1900242 regulation of synaptic vesicle endocytosis
GO:1900407 regulation of cellular response to oxidative stress
GO:1901526 positive regulation of mitophagy
GO:1901800 positive regulation of proteasomal protein catabolic process
GO:1902236 negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
GO:1902254 negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator
GO:1902530 positive regulation of protein linear polyubiquitination
GO:1903265 positive regulation of tumor necrosis factor-mediated signaling pathway
GO:1903377 negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway
GO:1903382 negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway
GO:1903427 negative regulation of reactive oxygen species biosynthetic process
GO:1903542 negative regulation of exosomal secretion
GO:1903861 positive regulation of dendrite extension
GO:1904049 negative regulation of spontaneous neurotransmitter secretion
GO:1904643 response to curcumin
GO:1904845 cellular response to L-glutamine
GO:1904881 cellular response to hydrogen sulfide
GO:1905232 cellular response to L-glutamate
GO:1905366 negative regulation of intralumenal vesicle formation
GO:1905477 positive regulation of protein localization to membrane
GO:2000377 regulation of reactive oxygen species metabolic process
GO:2000378 negative regulation of reactive oxygen species metabolic process
GO:2001171 positive regulation of ATP biosynthetic process
Cellular Component
GO:0000139 Golgi membrane
GO:0000151 ubiquitin ligase complex
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0008021 synaptic vesicle
GO:0014069 postsynaptic density
GO:0016235 aggresome
GO:0019005 SCF ubiquitin ligase complex
GO:0030424 axon
GO:0030672 synaptic vesicle membrane
GO:0032991 protein-containing complex
GO:0042995 cell projection
GO:0043005 neuron projection
GO:0043025 neuronal cell body
GO:0043195 terminal bouton
GO:0045202 synapse
GO:0048471 perinuclear region of cytoplasm
GO:0097708 intracellular vesicle
GO:0098691 dopaminergic synapse
GO:0098793 presynapse
GO:0098794 postsynapse
GO:0098978 glutamatergic synapse
GO:0099073 mitochondrion-derived vesicle
GO:1990452 Parkin-FBXW7-Cul1 ubiquitin ligase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4k95, PDBe:4k95, PDBj:4k95
PDBsum4k95
PubMed23661642
UniProtQ9JK66|PRKN_RAT E3 ubiquitin-protein ligase parkin (Gene Name=Prkn)

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