Structure of PDB 5yto Chain E Binding Site BS01

Receptor Information
>5yto Chain E (length=154) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHE
FGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSI
EDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVI
GIAQ
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 chain5yto Chain E Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5yto Assessment of ligand binding at a site relevant to SOD1 oxidation and aggregation
Resolution1.9 Å
Binding residue
(original residue number in PDB)		H63 H71 H80 D83
Binding residue
(residue number reindexed from 1)		H64 H72 H81 D84
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H46 H48 H63 H71 H80 D83 H120 R143
Catalytic site (residue number reindexed from 1) H47 H49 H64 H72 H81 D84 H121 R144
Enzyme Commision number 1.15.1.1: superoxide dismutase.
Gene Ontology
Molecular Function
GO:0004784 superoxide dismutase activity
GO:0005507 copper ion binding
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016209 antioxidant activity
GO:0016491 oxidoreductase activity
GO:0030346 protein phosphatase 2B binding
GO:0031267 small GTPase binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0051087 protein-folding chaperone binding
Biological Process
GO:0000302 response to reactive oxygen species
GO:0000303 response to superoxide
GO:0001541 ovarian follicle development
GO:0001819 positive regulation of cytokine production
GO:0001890 placenta development
GO:0001895 retina homeostasis
GO:0002262 myeloid cell homeostasis
GO:0006749 glutathione metabolic process
GO:0006801 superoxide metabolic process
GO:0006879 intracellular iron ion homeostasis
GO:0006915 apoptotic process
GO:0006979 response to oxidative stress
GO:0007283 spermatogenesis
GO:0007566 embryo implantation
GO:0007605 sensory perception of sound
GO:0007626 locomotory behavior
GO:0008089 anterograde axonal transport
GO:0008090 retrograde axonal transport
GO:0008217 regulation of blood pressure
GO:0008340 determination of adult lifespan
GO:0009408 response to heat
GO:0009410 response to xenobiotic stimulus
GO:0010467 gene expression
GO:0019226 transmission of nerve impulse
GO:0019228 neuronal action potential
GO:0019430 removal of superoxide radicals
GO:0032287 peripheral nervous system myelin maintenance
GO:0032930 positive regulation of superoxide anion generation
GO:0033081 regulation of T cell differentiation in thymus
GO:0035234 ectopic germ cell programmed cell death
GO:0040014 regulation of multicellular organism growth
GO:0042542 response to hydrogen peroxide
GO:0042554 superoxide anion generation
GO:0043065 positive regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
GO:0043087 regulation of GTPase activity
GO:0043410 positive regulation of MAPK cascade
GO:0043524 negative regulation of neuron apoptotic process
GO:0045471 response to ethanol
GO:0046620 regulation of organ growth
GO:0046716 muscle cell cellular homeostasis
GO:0048538 thymus development
GO:0048678 response to axon injury
GO:0050665 hydrogen peroxide biosynthetic process
GO:0050728 negative regulation of inflammatory response
GO:0050766 positive regulation of phagocytosis
GO:0051093 negative regulation of developmental process
GO:0051881 regulation of mitochondrial membrane potential
GO:0060047 heart contraction
GO:0060052 neurofilament cytoskeleton organization
GO:0060087 relaxation of vascular associated smooth muscle
GO:0060088 auditory receptor cell stereocilium organization
GO:0072593 reactive oxygen species metabolic process
GO:0099610 action potential initiation
GO:1902177 positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
GO:2000242 negative regulation of reproductive process
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005758 mitochondrial intermembrane space
GO:0005759 mitochondrial matrix
GO:0005777 peroxisome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0031410 cytoplasmic vesicle
GO:0032839 dendrite cytoplasm
GO:0032991 protein-containing complex
GO:0043025 neuronal cell body
GO:0070062 extracellular exosome
GO:1904115 axon cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yto, PDBe:5yto, PDBj:5yto
PDBsum5yto
PubMed29679384
UniProtP00441|SODC_HUMAN Superoxide dismutase [Cu-Zn] (Gene Name=SOD1)

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