Structure of PDB 5vf9 Chain A Binding Site BS01

Receptor Information
>5vf9 Chain A (length=199) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKHSLPDLPYDYGALEPHINAQIMQLHHSKHHAAYVNNLNVTEEKYQEAL
AKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKR
DFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGHLQIAACPNQDPLQGT
TGLIPLLGIDVWEHAYYLQYKNVRPDYLKAIWNVINWENVTERYMACKK
Ligand information
Ligand IDMN
InChIInChI=1S/Mn/q+2
InChIKeyWAEMQWOKJMHJLA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mn+2]
CACTVS 3.341[Mn++]
FormulaMn
NameMANGANESE (II) ION
ChEMBL
DrugBankDB06757
ZINC
PDB chain5vf9 Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vf9 Substrate-analog binding and electrostatic surfaces of human manganese superoxide dismutase.
Resolution1.82 Å
Binding residue
(original residue number in PDB)		H26 H74 D159 H163
Binding residue
(residue number reindexed from 1)		H27 H75 D160 H164
Annotation score1
Enzymatic activity
Enzyme Commision number 1.15.1.1: superoxide dismutase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004784 superoxide dismutase activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0019825 oxygen binding
GO:0019899 enzyme binding
GO:0030145 manganese ion binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0000302 response to reactive oxygen species
GO:0000303 response to superoxide
GO:0001666 response to hypoxia
GO:0001836 release of cytochrome c from mitochondria
GO:0001889 liver development
GO:0003032 detection of oxygen
GO:0003069 acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure
GO:0006357 regulation of transcription by RNA polymerase II
GO:0006749 glutathione metabolic process
GO:0006801 superoxide metabolic process
GO:0006979 response to oxidative stress
GO:0007005 mitochondrion organization
GO:0007507 heart development
GO:0007626 locomotory behavior
GO:0008217 regulation of blood pressure
GO:0008285 negative regulation of cell population proliferation
GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage
GO:0008631 intrinsic apoptotic signaling pathway in response to oxidative stress
GO:0008637 apoptotic mitochondrial changes
GO:0009410 response to xenobiotic stimulus
GO:0009791 post-embryonic development
GO:0010042 response to manganese ion
GO:0010043 response to zinc ion
GO:0010269 response to selenium ion
GO:0010332 response to gamma radiation
GO:0010729 positive regulation of hydrogen peroxide biosynthetic process
GO:0014823 response to activity
GO:0019430 removal of superoxide radicals
GO:0022904 respiratory electron transport chain
GO:0030097 hemopoiesis
GO:0030335 positive regulation of cell migration
GO:0031667 response to nutrient levels
GO:0032364 intracellular oxygen homeostasis
GO:0032496 response to lipopolysaccharide
GO:0033591 response to L-ascorbic acid
GO:0034021 response to silicon dioxide
GO:0034599 cellular response to oxidative stress
GO:0035900 response to isolation stress
GO:0035902 response to immobilization stress
GO:0042311 vasodilation
GO:0042542 response to hydrogen peroxide
GO:0042554 superoxide anion generation
GO:0042743 hydrogen peroxide metabolic process
GO:0043066 negative regulation of apoptotic process
GO:0043524 negative regulation of neuron apoptotic process
GO:0045429 positive regulation of nitric oxide biosynthetic process
GO:0045599 negative regulation of fat cell differentiation
GO:0046686 response to cadmium ion
GO:0048147 negative regulation of fibroblast proliferation
GO:0048666 neuron development
GO:0048678 response to axon injury
GO:0048773 erythrophore differentiation
GO:0050665 hydrogen peroxide biosynthetic process
GO:0051289 protein homotetramerization
GO:0051602 response to electrical stimulus
GO:0051881 regulation of mitochondrial membrane potential
GO:0055093 response to hyperoxia
GO:0060586 multicellular organismal-level iron ion homeostasis
GO:0071000 response to magnetism
GO:0071361 cellular response to ethanol
GO:0072593 reactive oxygen species metabolic process
GO:1902176 negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
GO:1902631 negative regulation of membrane hyperpolarization
GO:1904706 negative regulation of vascular associated smooth muscle cell proliferation
GO:1905461 positive regulation of vascular associated smooth muscle cell apoptotic process
GO:1905932 positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0042645 mitochondrial nucleoid
GO:0070062 extracellular exosome

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Biological Process
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Cellular Component
External links
PDB RCSB:5vf9, PDBe:5vf9, PDBj:5vf9
PDBsum5vf9
PubMed28461152
UniProtP04179|SODM_HUMAN Superoxide dismutase [Mn], mitochondrial (Gene Name=SOD2)

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